Result:
found more than 741 distributions - search limited to the first 2001 files matching your query
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Bio-Biblio
view release on metacpan or search on metacpan
eg/biblio-soap.pl view on Meta::CPAN
],
'pagination' => {
'medlinePgn' => '766-72'
},
'abstract' => {
'abstractText' => 'We show that induction of transcription of a CYC1-lacZ fusion gene, borne on a yeast plasmid, causes an increase in negative superhelicity of approximately five turns. This increase is abo...
},
'languages' => [
'eng'
],
'publicationTypes' => [
Bio-BigFile
view release on metacpan or search on metacpan
lib/Bio/DB/BigWigSet.pm view on Meta::CPAN
my ($current_path,%wigs);
while (<$f>) {
chomp;
s/\s+$//; # strip whitespace at ends of lines
# strip right-column comments unless they look like colors or html fragments
s/\s*\#.*$// unless /\#[0-9a-f]{6,8}\s*$/i || /\w+\#\w+/ || /\w+\"*\s*\#\d+$/;
if (/^\[([^\]]+)\]/) { # beginning of a configuration section
my $wigname = $1;
$current_path = $wigname =~ m!^(/|http:|ftp:)! ? $wigname
: "$base/$wigname";
Bio-BioVeL
view release on metacpan or search on metacpan
lib/Bio/BioVeL/Service.pm view on Meta::CPAN
}
}
=item handler
This method is triggered by mod_perl when a URL path fragment is encountered that matches
the mapping specified in httpd.conf. Example:
<Location /foo>
SetHandler perl-script
PerlResponseHandler Bio::BioVeL::Service::Foo
Bio-DB-GFF
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lib/Bio/DB/GFF.pm view on Meta::CPAN
follow this format, or grouping will not work properly.
=back
The sequences used to establish the coordinate system for annotations
can correspond to sequenced clones, clone fragments, contigs or
super-contigs. Thus, this module can be used throughout the lifecycle
of a sequencing project.
In addition to a group ID, the GFF format allows annotations to have a
group class. For example, in the ACeDB representation, RNA
lib/Bio/DB/GFF.pm view on Meta::CPAN
Here's an example to explain how this works:
my $db = Bio::DB::GFF->new(-dsn => 'dbi:mysql:human',-adaptor=>'dbi::mysql');
If successful, $db will now hold the database accessor object. We now
try to fetch the fragment of sequence whose ID is A0000182 and class
is "Accession."
my $segment = $db->segment(-name=>'A0000182',-class=>'Accession');
If successful, $segment now holds the entire segment corresponding to
Bio-DB-HTS
view release on metacpan or search on metacpan
lib/Bio/DB/HTS.pm view on Meta::CPAN
sub max_pileup_cnt {
my $self = shift;
return Bio::DB::HTSfile->max_pileup_cnt(@_);
}
# return a fragment of code that will be placed in the eval "" filter
# to eliminate alignments that don't match by name
sub _filter_by_name {
my $self = shift;
my $name = shift;
my $frag = "my \$name=\$a->qname; defined \$name or return; ";
if ( my $regexp = $self->_glob_match($name) ) {
$frag .= "return unless \$name =~ /^$regexp\$/i;\n";
}
else {
$frag .= "return unless lc \$name eq '$name';\n";
}
}
# return a fragment of code that will be placed in the eval "" filter
# to eliminate alignments that don't match by attribute
sub _filter_by_attribute {
my $self = shift;
my $attributes = shift;
my $result;
Bio-DB-NCBIHelper
view release on metacpan or search on metacpan
eg/gb2features.pl view on Meta::CPAN
Feature has tag organism with values, Homo sapiens
Feature has tag db_xref with values, taxon:9606
Feature from 1 to 31550 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 31651 to 48510 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 48611 to 64044 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 64145 to 78208 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 78309 to 89008 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 89109 to 99704 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 99805 to 107965 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 108066 to 116032 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 116133 to 124010 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 124111 to 130494 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 130595 to 136072 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 136173 to 139649 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 139750 to 144590 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 144691 to 148482 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 148583 to 152279 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 152380 to 153632 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment clone_end:T7
vector_side:left
Feature from 153733 to 155746 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 155847 to 156405 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment clone_end:SP6
vector_side:right
Feature from 156506 to 158398 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 158499 to 161333 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 161434 to 163304 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 163405 to 164604 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 164705 to 166693 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Feature from 166794 to 168978 Primary tag misc_feature, produced by
EMBL/GenBank/SwissProt
Feature on strand 1
Feature has tag note with values, assembly_fragment
Bio-DB-SeqFeature
view release on metacpan or search on metacpan
lib/Bio/DB/SeqFeature/Store.pm view on Meta::CPAN
Function: Inserts sequence data into the database at the indicated offset
Returns : true if successful
Args : see below
Status : public
This method inserts the DNA or protein sequence fragment
$sequence_string, identified by the ID $seq_id, into the database at
the indicated offset $offset. It is used internally by the GFF3Loader
to load sequence data from the files.
=cut
Bio-DB-TFBS
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lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
$annot->add_Annotation($sv);
return $seq;
}
=head2 get_fragment
Title : get_fragment
Usage : my $seq = $obj->get_fragment($id);
Function: Get the sequence of a fragment.
Returns : Bio::Seq
Args : string - a site id ('FR...')
=cut
sub get_fragment {
my ($self, $id) = @_;
$id || return;
my $data = $self->{fragment}->{data}->{$id} || return;
my @data = split(SEPARATOR, $data);
# accession = id gene_id1 gene_id2 species_tax_id_or_raw_string sequence source
return new Bio::Seq( -seq => $data[4],
-accession_number => $id,
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
sub get_factor_ids {
my $self = shift;
return $self->_get_ids('factor', @_);
}
=head2 get_fragment_ids
Title : get_fragment_ids
Usage : my @ids = $obj->get_fragment_ids(-key => $value);
Function: Get all the fragment ids that are associated with the supplied
args.
Returns : list of strings (ids)
Args : -key => value, where value is a string id, and key is one of:
-id -species -gene -factor -reference
=cut
sub get_fragment_ids {
my $self = shift;
return $self->_get_ids('fragment', @_);
}
=head2 Helper methods
=cut
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
my $index_dir = $self->index_directory;
my $gene_index = "$index_dir/gene.dat.index";
my $reference_index = "$index_dir/reference.dat.index";
my $matrix_index = "$index_dir/matrix.dat.index";
my $factor_index = "$index_dir/factor.dat.index";
my $fragment_index = "$index_dir/fragment.dat.index";
my $site_index = "$index_dir/site.dat.index";
my $reference_dat = "$dat_dir/reference.dat";
if (! -e $reference_index || $force) {
open my $REF, '<', $reference_dat or $self->throw("Could not read reference file '$reference_dat': $!");
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
my $reference_site = $site_index.'.reference';
unlink $reference_site;
my $site = tie(%site, 'DB_File', $reference_site, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$reference_site': $!");
my %fragment;
my $reference_fragment = $fragment_index.'.reference';
unlink $reference_fragment;
my $fragment = tie(%fragment, 'DB_File', $reference_fragment, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$reference_fragment': $!");
my %factor;
my $reference_factor = $factor_index.'.reference';
unlink $reference_factor;
my $factor = tie(%factor, 'DB_File', $reference_factor, O_RDWR|O_CREAT, 0644, $DB_BTREE)
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
}
elsif (/^FA TRANSFAC: (\w\d+)/) {
$factor->put($data[0], "$1");
}
elsif (/^FR TRANSFAC: (FR\d+)/) {
$fragment->put($data[0], "$1");
}
elsif (/^MX TRANSFAC: (\w\d+)/) {
$matrix->put($data[0], "$1");
}
elsif (/^\/\//) {
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
@data = ();
}
}
close $REF;
$ref = $pub = $gene = $site = $fragment = $factor = $matrix = undef;
untie %references;
untie %pubmed;
untie %gene;
untie %site;
untie %fragment;
untie %factor;
untie %matrix;
}
my $gene_dat = "$dat_dir/gene.dat";
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
my $gene_factor = $factor_index.'.gene';
unlink $gene_factor;
my $factor = tie(%factor, 'DB_File', $gene_factor, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$gene_factor': $!");
my %fragment;
my $gene_fragment = $fragment_index.'.gene';
unlink $gene_fragment;
my $fragment = tie(%fragment, 'DB_File', $gene_fragment, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$gene_fragment': $!");
my %reference;
my $gene_reference = $reference_index.'.gene';
unlink $gene_reference;
my $reference = tie(%reference, 'DB_File', $gene_reference, O_RDWR|O_CREAT, 0644, $DB_BTREE)
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
}
elsif (/^FA (T\d+)/) {
$factor->put($data[0], "$1");
}
elsif (/^BR (FR\d+)/) {
$fragment->put($data[0], "$1");
}
elsif (/^\/\//) {
# end of a record, store previous data and reset
# accession = id name description species_tax_id_or_raw_string
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
my $factor_site = $site_index.'.factor';
unlink $factor_site;
my $site = tie(%site, 'DB_File', $factor_site, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$factor_site': $!");
my %fragment;
my $factor_fragment = $fragment_index.'.factor';
unlink $factor_fragment;
my $fragment = tie(%fragment, 'DB_File', $factor_fragment, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$factor_fragment': $!");
my %reference;
my $factor_reference = $reference_index.'.factor';
unlink $factor_reference;
my $reference = tie(%reference, 'DB_File', $factor_reference, O_RDWR|O_CREAT, 0644, $DB_BTREE)
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
}
elsif (/^BS (R\d+)/) {
$site->put($data[0], "$1");
}
elsif (/^BR (FR\d+)/) {
$fragment->put($data[0], "$1");
}
elsif (/^RN .+?(RE\d+)/) {
$reference->put($data[0], "$1");
}
elsif (/^\/\//) {
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
$sequence = '';
}
}
close $FAC;
$factor = $id = $name = $species = $interact = $gene = $matrix = $site = $fragment = $reference = undef;
untie %factors;
untie %id;
untie %name;
untie %species;
untie %interactors;
untie %gene;
untie %matrix;
untie %site;
untie %fragment;
untie %reference;
}
my $fragment_dat = "$dat_dir/fragment.dat";
if (! -e $fragment_index || $force) {
if (open my $FRA, '<', $fragment_dat) {
my %fragments;
unlink $fragment_index;
my $fragment = tie(%fragments, 'DB_File', $fragment_index, O_RDWR|O_CREAT, 0644, $DB_HASH)
or $self->throw("Could not open file '$fragment_index': $!");
my %id;
my $fragment_id = $fragment_index.'.id';
unlink $fragment_id;
my $id = tie(%id, 'DB_File', $fragment_id, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$fragment_id': $!");
my %qualities;
my $fragment_qualities = $fragment_index.'.qual';
unlink $fragment_qualities;
my $quality = tie(%qualities, 'DB_File', $fragment_qualities, O_RDWR|O_CREAT, 0644, $DB_HASH)
or $self->throw("Could not open file '$fragment_qualities': $!");
my %species;
my $fragment_species = $fragment_index.'.species';
unlink $fragment_species;
my $species = tie(%species, 'DB_File', $fragment_species, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$fragment_species': $!");
my %gene;
my $fragment_gene = $gene_index.'.fragment';
unlink $fragment_gene;
my $gene = tie(%gene, 'DB_File', $fragment_gene, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$fragment_gene': $!");
my %factor;
my $fragment_factor = $factor_index.'.fragment';
unlink $fragment_factor;
my $factor = tie(%factor, 'DB_File', $fragment_factor, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$fragment_factor': $!");
my %reference;
my $fragment_reference = $reference_index.'.fragment';
unlink $fragment_reference;
my $reference = tie(%reference, 'DB_File', $fragment_reference, O_RDWR|O_CREAT, 0644, $DB_BTREE)
or $self->throw("Could not open file '$fragment_reference': $!");
# skip the first three header lines
<$FRA>; <$FRA>; <$FRA>;
my @data;
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
}
elsif (/^\/\//) {
# end of a record, store previous data and reset
# accession = id gene_id1 gene_id2 species_tax_id_or_raw_string sequence source
$fragments{$data[0]} = join(SEPARATOR, ($data[1] || '',
$data[2] || '',
$data[3] || '',
$data[4] || '',
$data[5] || '',
$data[6] || ''));
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
@data = ();
}
}
close $FRA;
$fragment = $id = $species = $quality = $gene = $factor = $reference = undef;
untie %fragments;
untie %id;
untie %species;
untie %qualities;
untie %gene;
untie %factor;
untie %reference;
}
else {
$self->warn("Could not read fragment file '$fragment_dat', assuming you have an old version of Transfac Pro with no fragment.dat file");
}
}
}
# connect the internal db handle
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
my $gene_index = "$index_dir/gene.dat.index";
my $reference_index = "$index_dir/reference.dat.index";
my $matrix_index = "$index_dir/matrix.dat.index";
my $factor_index = "$index_dir/factor.dat.index";
my $site_index = "$index_dir/site.dat.index";
my $fragment_index = "$index_dir/fragment.dat.index";
foreach ($gene_index, $reference_index, $matrix_index, $factor_index, $site_index, $fragment_index) {
if (! -e $_) {
#$self->warn("Index files have not been created");
#return 0;
}
}
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
$self->{gene}->{reference} = tie (%{$self->{gene}->{reference}}, 'DB_File', $reference_gene, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$reference_gene': $!");
my $reference_site = $site_index.'.reference';
$self->{site}->{reference} = tie (%{$self->{site}->{reference}}, 'DB_File', $reference_site, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$reference_site': $!");
my $reference_fragment = $fragment_index.'.reference';
$self->{fragment}->{reference} = tie (%{$self->{fragment}->{reference}}, 'DB_File', $reference_fragment, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$reference_fragment': $!");
my $reference_factor = $factor_index.'.reference';
$self->{factor}->{reference} = tie (%{$self->{factor}->{reference}}, 'DB_File', $reference_factor, undef, 0644, $DB_BTREE) || $self->throw("Cannot open file '$reference_factor': $!");
my $reference_matrix = $matrix_index.'.reference';
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
$self->{gene}->{species} = tie(%{$self->{gene}->{species}}, 'DB_File', $gene_species, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$gene_species': $!");
my $gene_site = $site_index.'.gene';
$self->{site}->{gene} = tie(%{$self->{site}->{gene}}, 'DB_File', $gene_site, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$gene_site': $!");
my $gene_fragment = $fragment_index.'.gene';
$self->{fragment}->{gene} = tie(%{$self->{fragment}->{gene}}, 'DB_File', $gene_fragment, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$gene_fragment': $!");
my $gene_factor = $factor_index.'.gene';
$self->{factor}->{gene} = tie(%{$self->{factor}->{gene}}, 'DB_File', $gene_factor, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$gene_factor': $!");
my $gene_reference = $reference_index.'.gene';
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
my $site_reference = $reference_index.'.site';
$self->{reference}->{site} = tie(%{$self->{reference}->{site}}, 'DB_File', $site_reference, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$site_reference': $!");
}
# fragment (may not be in older databases)
if (-e $fragment_index) {
$self->{fragment}->{data} = {};
tie (%{$self->{fragment}->{data}}, 'DB_File', $fragment_index, O_RDWR, undef, $DB_HASH) || $self->throw("Cannot open file '$fragment_index': $!");
my $fragment_id = $fragment_index.'.id';
$self->{fragment}->{id} = tie(%{$self->{fragment}->{id}}, 'DB_File', $fragment_id, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$fragment_id': $!");
my $fragment_species = $fragment_index.'.species';
$self->{fragment}->{species} = tie(%{$self->{fragment}->{species}}, 'DB_File', $fragment_species, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file $fragment_species': $!");
#*** quality not actually used by anything (yet)
my $fragment_qualities = $fragment_index.'.qual';
$self->{fragment_quality} = {};
tie(%{$self->{fragment_quality}}, 'DB_File', $fragment_qualities, O_RDWR, undef, $DB_HASH) || $self->throw("Cannot open file '$fragment_qualities': $!");
my $fragment_gene = $gene_index.'.fragment';
$self->{gene}->{fragment} = tie(%{$self->{gene}->{fragment}}, 'DB_File', $fragment_gene, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$fragment_gene': $!");
my $fragment_factor = $factor_index.'.fragment';
$self->{factor}->{fragment} = tie(%{$self->{factor}->{fragment}}, 'DB_File', $fragment_factor, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$fragment_factor': $!");
my $fragment_reference = $reference_index.'.fragment';
$self->{reference}->{fragment} = tie(%{$self->{reference}->{fragment}}, 'DB_File', $fragment_reference, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$fragment_reference': $!");
}
else {
die "no fragment_index at '$fragment_index'\n";
}
# matrix
{
$self->{matrix}->{data} = {};
lib/Bio/DB/TFBS/transfac_pro.pm view on Meta::CPAN
$self->{matrix}->{factor} = tie(%{$self->{matrix}->{factor}}, 'DB_File', $factor_matrix, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$factor_matrix': $!");
my $factor_site = $site_index.'.factor';
$self->{site}->{factor} = tie(%{$self->{site}->{factor}}, 'DB_File', $factor_site, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$factor_site': $!");
my $factor_fragment = $fragment_index.'.factor';
$self->{fragment}->{factor} = tie(%{$self->{fragment}->{factor}}, 'DB_File', $factor_fragment, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$factor_fragment': $!");
my $factor_reference = $reference_index.'.factor';
$self->{reference}->{factor} = tie(%{$self->{reference}->{factor}}, 'DB_File', $factor_reference, O_RDWR, undef, $DB_BTREE) || $self->throw("Cannot open file '$factor_reference': $!");
}
Bio-Das
view release on metacpan or search on metacpan
In a scalar context, results() will return a hashref in which the keys
are the segment strings passed to the request with the B<-segments>
argument and the values are arrayrefs containing the list of results.
There is an equivalence here. When this code fragment executes, both
$results_hash1 and $results_hash2 will contain the same information.
my @results = $request->results;
my $result_hash1 = {};
for my $r (@results) {
Bio-EBI-RNAseqAPI
view release on metacpan or search on metacpan
inc/Module/AutoInstall.pm view on Meta::CPAN
return 1;
}
sub postamble {
$PostambleUsed = 1;
my $fragment;
$fragment .= <<"AUTO_INSTALL" if !$InstallDepsTarget;
config :: installdeps
\t\$(NOECHO) \$(NOOP)
AUTO_INSTALL
$fragment .= <<"END_MAKE";
checkdeps ::
\t\$(PERL) $0 --checkdeps
installdeps ::
inc/Module/AutoInstall.pm view on Meta::CPAN
listalldeps ::
\t$PostambleActionsListAllDeps
END_MAKE
return $fragment;
}
1;
__END__
Bio-EnsEMBL
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lib/Bio/EnsEMBL/Utils/AssemblyProjector.pm view on Meta::CPAN
the database for this to work, see the 'Related Modules' section below
on how to generate the mapping.
In addition to the "raw" projecting of features and slices, the methods
in this module also apply some sensible rules to the results of the
projection (like discarding unwanted results or merging fragmented
projections). These are the rules (depending on configuration):
Discard the projected feature/slice if:
1. it doesn't project at all (no segments returned)
2. [unless MERGE_FRAGMENTS is set] the projection is fragmented (more
than one segment)
3. [if CHECK_LENGTH is set] the projection doesn't have the same
length as the original feature/slice
4. all segments are on same chromosome and strand
lib/Bio/EnsEMBL/Utils/AssemblyProjector.pm view on Meta::CPAN
new_to_old
adaptor
external_source
old_assembly
new_assembly
merge_fragments
check_length
=head1 RELATED MODULES
The process of creating a whole genome alignment between two assemblies
lib/Bio/EnsEMBL/Utils/AssemblyProjector.pm view on Meta::CPAN
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my ($adaptor, $external_source, $old_assembly, $new_assembly,
$merge_fragments, $check_length) = rearrange([qw(ADAPTOR EXTERNAL_SOURCE
OLD_ASSEMBLY NEW_ASSEMBLY MERGE_FRAGMENTS CHECK_LENGTH)], @_);
unless ($adaptor and ref($adaptor) and
$adaptor->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')) {
throw("You must provide a DBAdaptor to a database containing the assembly mapping.");
lib/Bio/EnsEMBL/Utils/AssemblyProjector.pm view on Meta::CPAN
# initialise
$self->adaptor($adaptor);
$self->{'old_assembly'} = $old_assembly;
$self->{'new_assembly'} = $new_assembly;
# by default, merge fragments
$self->{'merge_fragments'} = $merge_fragments || 1;
# by default, do not check length
$self->{'check_length'} = $check_length || 0;
# by default, features and slices are expected in same database as the
lib/Bio/EnsEMBL/Utils/AssemblyProjector.pm view on Meta::CPAN
# apply rules to projection results
#
# discard the projected feature/slice if
# 1. it doesn't project at all (no segments returned)
# 2. [unless MERGE_FRAGMENTS is set] the projection is fragmented (more
# than one segment)
# 3. [if CHECK_LENGTH is set] the projection doesn't have the same length
# as the original feature/slice
# 4. all segments are on same chromosome and strand
lib/Bio/EnsEMBL/Utils/AssemblyProjector.pm view on Meta::CPAN
# test (1)
return undef unless (@segments);
#warn "DEBUG: passed test 1\n";
# test (2)
return undef if (!($self->merge_fragments) and scalar(@segments) > 1);
push @status, 'fragmented' if (scalar(@segments) > 1);
#warn "DEBUG: passed test 2\n";
# test (3)
my $first_slice = $segments[0]->to_Slice;
my $last_slice = $segments[-1]->to_Slice;
lib/Bio/EnsEMBL/Utils/AssemblyProjector.pm view on Meta::CPAN
$self->{'new_assembly'} = shift if (@_);
return $self->{'new_assembly'};
}
sub merge_fragments {
my $self = shift;
$self->{'merge_fragments'} = shift if (@_);
return $self->{'merge_fragments'};
}
sub check_length {
my $self = shift;
Bio-GMOD
view release on metacpan or search on metacpan
GMOD/StandardURLs.pm view on Meta::CPAN
Leads to the index for the most recent release, symbolic link style.
=item http://your.site/genome/Binomial_name/current/dna
Returns a FASTA file containing big DNA fragments
(e.g. chromosomes). MIME type is application/x-fasta.
=item http://your.site/genome/Binomial_name/current/mrna
Returns a FASTA file containing spliced mRNA transcript
Bio-Genex
view release on metacpan or search on metacpan
data/controlled_vocab/ALS_SpotTypeWannabe.xml.new view on Meta::CPAN
<term name="synthetic_oligo"
description="a synthetic DNA oligomer, sequence as described"/>
<term name="pcr_product"
description="the amplified section of a an EST, full-length cDNA or other sequence feature"/>
<term name="gdna_sequence"
description="the sequence of a fragment derived from a genomic source"/>
<term name="control_intensity_range"
description="allows the dynamic range of signal detection to be estimated"/>
<term name="control_nonspecific_binding"
description="Allows the noise from non-specific binding to be estimated"/>
<term name="control_target_concentration"
Bio-GenomeMap
view release on metacpan or search on metacpan
Chr1 TAIR8 exon 11649 13173 7 - . Parent=AT1G01030.1
Chr1 TAIR8 gene 11649 13714 7 - . ID=AT1G01030;Note=protein_coding_gene;Name=AT1G01030
Chr1 TAIR8 protein 11864 12940 5 - . ID=AT1G01030.1-Protein;Name=AT1G01030.1;Derives_from=AT1G01030.1
Chr1 TAIR8 transposable_element 11897 11976 7 + . ID=AT1TE00010;Name=AT1TE00010;Alias=ATCOPIA24
Chr1 TAIR8 five_prime_UTR 13335 13714 2 - . Parent=AT1G01030.1
Chr1 TAIR8 transposon_fragment 17024 18330 2 + . Parent=AT1TE00025
Chr1 TAIR8 transposable_element 17024 18924 2 + . ID=AT1TE00025;Name=AT1TE00025;Alias=ATREP3
Chr1 TAIR8 transposable_element 18331 18642 8 - . ID=AT1TE00030;Name=AT1TE00030;Alias=ATHATN7
Chr1 TAIR8 transposon_fragment 18643 18924 1 + . Parent=AT1TE00025
Chr1 TAIR8 five_prime_UTR 23146 23518 3 + . Parent=AT1G01040.1
Chr1 TAIR8 exon 23146 24451 8 + . Parent=AT1G01040.1
Chr1 TAIR8 gene 23146 31227 4 + . ID=AT1G01040;Note=protein_coding_gene;Name=AT1G01040
Chr1 TAIR8 protein 23519 31079 1 + . ID=AT1G01040.1-Protein;Name=AT1G01040.1;Derives_from=AT1G01040.1
Chr1 TAIR8 exon 24542 24655 1 + . Parent=AT1G01040.1
Chr1 TAIR8 protein 53022 54494 4 + . ID=AT1G01110.1-Protein;Name=AT1G01110.1;Derives_from=AT1G01110.1
Chr1 TAIR8 exon 53484 53624 2 + . Parent=AT1G01110.1
Chr1 TAIR8 CDS 53703 54494 2 + 0 Parent=AT1G01110.1,AT1G01110.1-Protein;
Chr1 TAIR8 exon 53703 54692 7 + . Parent=AT1G01110.2
Chr1 TAIR8 three_prime_UTR 54495 54692 7 + . Parent=AT1G01110.2
Chr1 TAIR8 transposon_fragment 55874 56576 2 + . Parent=AT1TE00150
Chr1 TAIR8 gene 57269 59167 2 - . ID=AT1G01120;Note=protein_coding_gene;Name=AT1G01120
Chr1 TAIR8 protein 57392 58978 3 - . ID=AT1G01120.1-Protein;Name=AT1G01120.1;Derives_from=AT1G01120.1
Chr1 TAIR8 five_prime_UTR 58979 59167 7 - . Parent=AT1G01120.1
Chr1 TAIR8 CDS 61963 62124 6 - 0 Parent=AT1G01130.1,AT1G01130.1-Protein;
Chr1 TAIR8 gene 61963 63811 8 - . ID=AT1G01130;Note=protein_coding_gene;Name=AT1G01130
Chr2 TAIR8 gene 1871 2111 5 + . ID=AT2G01008;Note=other_RNA;Name=AT2G01008
Chr2 TAIR8 gene 3706 5513 7 + . ID=AT2G01010;Note=rRNA;Name=AT2G01010
Chr2 TAIR8 gene 6571 6672 2 + . ID=AT2G01021;Note=protein_coding_gene;Name=AT2G01021
Chr2 TAIR8 gene 9648 9767 8 - . ID=AT2G01023;Note=protein_coding_gene;Name=AT2G01023
Chr2 TAIR8 transposable_element_gene 10478 12861 8 - . ID=AT2G01022;Note=transposable_element_gene;Name=AT2G01022;Derives_from=AT2TE00010
Chr2 TAIR8 transposon_fragment 10524 12820 7 - . Parent=AT2TE00010
Chr2 TAIR8 transposon_fragment 12823 13069 8 - . Parent=AT2TE00010
Chr2 TAIR8 transposable_element 13072 29426 8 - . ID=AT2TE00015;Name=AT2TE00015;Alias=ATGP2
Chr2 TAIR8 transposable_element_gene 14395 16377 8 - . ID=AT2G01024;Note=transposable_element_gene;Name=AT2G01024;Derives_from=AT2TE00015
Chr2 TAIR8 transposable_element_gene 17624 22540 8 - . ID=AT2G01026;Note=transposable_element_gene;Name=AT2G01026;Derives_from=AT2TE00015
Chr2 TAIR8 transposable_element_gene 23971 26923 4 - . ID=AT2G01028;Note=transposable_element_gene;Name=AT2G01028;Derives_from=AT2TE00015
Chr2 TAIR8 transposon_fragment 28160 29426 1 - . Parent=AT2TE00015
Chr2 TAIR8 transposable_element_gene 28465 38652 9 + . ID=AT2G01029;Note=transposable_element_gene;Name=AT2G01029
Chr2 TAIR8 transposable_element 29428 30317 3 + . ID=AT2TE00020;Name=AT2TE00020;Alias=ATLANTYS3
Chr2 TAIR8 transposable_element 30318 31444 5 + . ID=AT2TE00025;Name=AT2TE00025;Alias=ATLANTYS1
Chr2 TAIR8 transposon_fragment 31445 31474 2 + . Parent=AT2TE00030
Chr2 TAIR8 transposable_element 31445 42029 1 + . ID=AT2TE00030;Name=AT2TE00030;Alias=ATLANTYS3
Chr2 TAIR8 transposable_element 31487 33553 9 + . ID=AT2TE00035;Name=AT2TE00035;Alias=ATGP2N
Chr2 TAIR8 transposon_fragment 33511 33553 9 + . Parent=AT2TE00035
Chr2 TAIR8 transposable_element 34294 34346 2 + . ID=AT2TE00040;Name=AT2TE00040;Alias=ATGP2
Chr2 TAIR8 transposable_element 34380 36436 1 + . ID=AT2TE00045;Name=AT2TE00045;Alias=ATGP2N
Chr2 TAIR8 transposon_fragment 36437 40847 4 + . Parent=AT2TE00030
Chr2 TAIR8 exon 39519 39776 5 - . Parent=AT2G01031.1
Chr2 TAIR8 transposable_element_gene 39519 40358 2 - . ID=AT2G01031;Note=transposable_element_gene;Name=AT2G01031;Derives_from=AT2TE00030
Chr2 TAIR8 transposon_fragment 40847 41197 4 + . Parent=AT2TE00030
Chr2 TAIR8 transposon_fragment 41178 42029 7 + . Parent=AT2TE00030
Chr2 TAIR8 transposable_element 42034 42128 4 - . ID=AT2TE00070;Name=AT2TE00070;Alias=ATLANTYS3
Chr2 TAIR8 transposable_element 42129 49796 7 - . ID=AT2TE00075;Name=AT2TE00075;Alias=ATGP2
Chr2 TAIR8 transposable_element_gene 43427 48350 6 - . ID=AT2G01034;Note=transposable_element_gene;Name=AT2G01034;Derives_from=AT2TE00075
Chr2 TAIR8 transposable_element 49819 49859 1 - . ID=AT2TE00080;Name=AT2TE00080;Alias=ATLANTYS3
Chr2 TAIR8 transposable_element 49860 50285 4 - . ID=AT2TE00085;Name=AT2TE00085;Alias=ATLANTYS3
Chr2 TAIR8 transposable_element 52105 52383 6 - . ID=AT2TE00090;Name=AT2TE00090;Alias=TAT1_ATH
Chr2 TAIR8 transposable_element 52644 58681 3 - . ID=AT2TE00095;Name=AT2TE00095;Alias=ATLANTYS3
Chr2 TAIR8 transposable_element 55136 55394 3 + . ID=AT2TE00100;Name=AT2TE00100;Alias=VANDAL6
Chr2 TAIR8 transposon_fragment 55589 56257 9 - . Parent=AT2TE00095
Chr2 TAIR8 transposon_fragment 58134 58681 1 - . Parent=AT2TE00095
Chr2 TAIR8 transposable_element 58682 64005 7 - . ID=AT2TE00110;Name=AT2TE00110;Alias=ATGP2
Chr2 TAIR8 transposable_element_gene 58705 64872 1 - . ID=AT2G01037;Note=transposable_element_gene;Name=AT2G01037;Derives_from=AT2TE00110
Chr2 TAIR8 transposon_fragment 64006 65070 9 - . Parent=AT2TE00115
Chr2 TAIR8 transposable_element_gene 65436 67139 6 - . ID=AT2G01040;Note=transposable_element_gene;Name=AT2G01040;Derives_from=AT2TE00120
Chr2 TAIR8 transposon_fragment 67095 68112 7 - . Parent=AT2TE00115
Chr2 TAIR8 gene 68337 69884 2 - . ID=AT2G01050;Note=protein_coding_gene;Name=AT2G01050
Chr2 TAIR8 transposable_element 70796 71407 8 + . ID=AT2TE00135;Name=AT2TE00135;Alias=ATREP3
Chr2 TAIR8 transposable_element 71652 71802 8 - . ID=AT2TE00140;Name=AT2TE00140;Alias=ATDNAI27T9C
Chr2 TAIR8 transposable_element 71803 72196 9 - . ID=AT2TE00145;Name=AT2TE00145;Alias=LIMPET1
Chr2 TAIR8 transposable_element 72206 72240 5 - . ID=AT2TE00150;Name=AT2TE00150;Alias=ATDNAI27T9C
Bio-Graphics
view release on metacpan or search on metacpan
lib/Bio/Graphics/FeatureFile.pm view on Meta::CPAN
=head2 Comments
Lines that begin with the # sign are treated as comments and
ignored. When a # sign appears within a line, everything to the right
of the symbol is also ignored, unless it looks like an HTML fragment or
an HTML color, e.g.:
# this is ignored
[Example]
glyph = generic # this comment is ignored
lib/Bio/Graphics/FeatureFile.pm view on Meta::CPAN
sub parse_config_line {
my $self = shift;
local $_ = shift;
# strip right-column comments unless they look like colors or html fragments
s/\s*\#.*$// unless /\#[0-9a-f]{6,8}\s*$/i || /\w+\#\w+/ || /\w+\"*\s*\#\d+$/;
if (/^\s+(.+)/ && $self->{current_tag}) { # configuration continuation line
my $value = $1;
my $cc = $self->{current_config} ||= 'general'; # in case no configuration named
Bio-Homology-InterologWalk
view release on metacpan or search on metacpan
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0400 ! affinity technology
[Term]
id: MI:0009
name: bacterial display
def: "The protein of interest is presented on the outer membrane of Gram negative bacteria by expressing it as a fusion partner to peptide signals that direct heterologous proteins to the cell surface. For instance, a single chain Fv (scFv) antibody ...
subset: PSI-MI slim
is_a: MI:0034 ! display technology
is_a: MI:0054 ! fluorescence-activated cell sorting
[Term]
id: MI:0010
name: beta galactosidase complementation
def: "Beta-galactosidase activity can be used to monitor the interaction of chimeric proteins. Pairs of inactive beta gal deletion mutants are capable of complementing to restore activity when fused to interacting protein partners. Critical to the su...
subset: PSI-MI slim
synonym: "beta galactosidase" EXACT PSI-MI-short []
is_a: MI:0228 ! cytoplasmic complementation assay
[Term]
id: MI:0011
name: beta lactamase complementation
def: "This strategy is based on a protein fragment complementation assay (PCA) of the enzyme TEM-1 beta-lactamase. The approach includes a simple colorimetric in vitro assays using the cephalosporin nitrocefin and assays in intact cells using the flu...
subset: PSI-MI slim
synonym: "beta lactamase" EXACT PSI-MI-short []
is_a: MI:0228 ! cytoplasmic complementation assay
[Term]
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0045 ! experimental interaction detection
[Term]
id: MI:0014
name: adenylate cyclase complementation
def: "Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary co...
subset: PSI-MI slim
synonym: "adenylate cyclase" EXACT PSI-MI-short []
synonym: "bacterial two-hybrid" EXACT PSI-MI-alternate []
is_a: MI:0228 ! cytoplasmic complementation assay
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0030 ! cross-linking study
[Term]
id: MI:0032
name: de novo protein sequencing by mass spectrometry
def: "The strategy to determine the complete amino acid sequence of a protein by mass spectrometry relies on the generation of a nested set of fragments differing by one amino acid. This reveals the identity of the residue that has been removed at ea...
subset: PSI-MI slim
synonym: "ms protein sequence" EXACT PSI-MI-short []
synonym: "MS/MS" RELATED []
is_a: MI:0093 ! protein sequence identification
is_a: MI:0427 ! Identification by mass spectrometry
is_a: MI:0659 ! experimental feature detection
[Term]
id: MI:0033
name: deletion analysis
def: "In this approach, once a molecule is demonstrated to participate in an interaction, several deletion derivatives are produced and tested in the binding assay to identify the minimal fragment (domain) that can still support the interaction." [PM...
subset: PSI-MI slim
is_a: MI:0074 ! mutation analysis
[Term]
id: MI:0034
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0067 ! light scattering
[Term]
id: MI:0039
name: edman degradation
def: "In this procedure the N-terminus amino acid is cleaved from a polypeptide and identified by high-pressure liquid chromatography. The cycle is repeated on the ever-shortening polypeptide until all the residues are identified. On average only 20-...
subset: PSI-MI slim
is_a: MI:0433 ! partial identification of protein sequence
[Term]
id: MI:0040
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0892 ! solid phase assay
[Term]
id: MI:0048
name: filamentous phage display
def: "Filamentous phages (M13, f1, fd) have been extensively used to develop and implement the technology of phage display. Repertoires of relatively short peptides of random amino acid sequences or cDNA libraries have been constructed and searched s...
subset: PSI-MI slim
synonym: "filamentous phage" EXACT PSI-MI-short []
is_a: MI:0084 ! phage display
[Term]
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0051 ! fluorescence technology
[Term]
id: MI:0056
name: full identification by DNA sequencing
def: "Sequencing occurs during the course of the experiment. The DNA to be sequenced is used as template for the in vitro synthesis, by DNA polymerase, of a set of partial replicas, all beginning at the same place, but terminating at different points...
subset: PSI-MI slim
synonym: "full dna sequence" EXACT PSI-MI-short []
is_a: MI:0078 ! nucleotide sequence identification
is_a: MI:0659 ! experimental feature detection
scripts/Data/psi-mi.obo view on Meta::CPAN
is_obsolete: true
[Term]
id: MI:0060
name: ha tag coimmunoprecipitation
def: "The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemaglutinin protein) for which antibodies are commercially available.\nOBSOLETE redundant term. Map to feature type : ha-tagged (MI:0520) an...
subset: PSI-MI slim
synonym: "ha tag coip" EXACT PSI-MI-short []
is_obsolete: true
[Term]
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0659 ! experimental feature detection
[Term]
id: MI:0075
name: myc tag coimmunoprecipitation
def: "The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.\nOBSOLETE redundan...
subset: PSI-MI slim
synonym: "myc tag coip " EXACT PSI-MI-short []
is_obsolete: true
[Term]
scripts/Data/psi-mi.obo view on Meta::CPAN
is_obsolete: true
[Term]
id: MI:0080
name: partial dna sequence identification by hybridization
def: "Genes are recognised by hybridization of a probe with a fragment of the gene sequence." [PMID:14755292]
subset: PSI-MI slim
synonym: "partial dna sequence" EXACT PSI-MI-short []
is_a: MI:0078 ! nucleotide sequence identification
[Term]
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0008 ! array technology
[Term]
id: MI:0082
name: peptide massfingerprinting
def: "This approach leads to protein identification by matching peptide masses, as measured by mass spectrometry, to the ones calculated from in silico fragmentation of a protein sequence database. A peptide mixture from a tryptic digest is analysed ...
subset: PSI-MI slim
synonym: "fingerprinting" EXACT PSI-MI-short []
is_a: MI:0427 ! Identification by mass spectrometry
is_a: MI:0433 ! partial identification of protein sequence
is_a: MI:0815 ! confirmation by molecular weight
[Term]
id: MI:0083
name: peptide synthesis
def: "When one of the partners participates in the interaction with a relatively short peptide fragment, it is often convenient to precisely identify the minimal region that supports the interaction by synthesising a series of overlapping peptides an...
subset: PSI-MI slim
is_a: MI:0093 ! protein sequence identification
[Term]
id: MI:0084
name: phage display
def: "Peptide sequences or entire proteins can be displayed on phage capsids by fusion to coat proteins to generate a library of fusion phages each displaying a different peptide. Such a library can then be exploited to identify specific phages that ...
subset: PSI-MI slim
is_a: MI:0034 ! display technology
[Term]
id: MI:0085
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0008 ! array technology
[Term]
id: MI:0090
name: protein complementation assay
def: "The function of numerous proteins or ribonucleic particles (enzymes, transcription factors, and others) can be rationally dissected into two fragments that fold autonomously but cannot complement to reconstitute the complex function, unless the...
subset: PSI-MI slim
synonym: "complementation" EXACT PSI-MI-short []
synonym: "PCA" EXACT PSI-MI-alternate []
is_a: MI:0045 ! experimental interaction detection
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0401 ! biochemical
[Term]
id: MI:0092
name: protein in situ array
def: "Protein In Situ Array is a method by which protein arrays are rapidly generated in one step directly from DNA, by cell-free protein expression and simultaneous in situ immobilisation at a surface. Individual genes or fragments are produce by PC...
subset: PSI-MI slim
synonym: "PISA" EXACT PSI-MI-alternate []
synonym: "pisa" EXACT PSI-MI-short []
is_a: MI:0089 ! protein array
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0063 ! interaction prediction
[Term]
id: MI:0102
name: sequence tag identification
def: "This approach leads to protein identification by combining mass measurement and short amino acid sequence information obtained by tandem mass spectrometry. This information is then used to automatically find the best match in a sequence databas...
subset: PSI-MI slim
synonym: "sequence tag" EXACT PSI-MI-short []
is_a: MI:0427 ! Identification by mass spectrometry
is_a: MI:0433 ! partial identification of protein sequence
[Term]
id: MI:0103
name: southern blot
def: "A standard procedure to identify DNA fragments containing specific gene sequences. In this procedure i) a genome is fragmented using a restriction enzyme ii) the generated fragments are separated by electrophoresis iii) the fragments are transf...
subset: PSI-MI slim
is_a: MI:0080 ! partial dna sequence identification by hybridization
[Term]
id: MI:0104
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0046 ! experimental knowledge based
[Term]
id: MI:0111
name: dihydrofolate reductase reconstruction
def: "The gene for DHFR is rationally dissected into two fragments called F[1,2] and F[3]. Two proteins or protein domains that are thought to bind to each other can then be fused to either of the two DHFR fragments. Reconstitution of enzyme activity...
subset: PSI-MI slim
synonym: "dhfr reconstruction" EXACT PSI-MI-short []
is_a: MI:0228 ! cytoplasmic complementation assay
[Term]
id: MI:0112
name: ubiquitin reconstruction
def: "In this method the two proteins, whose interaction is under investigation, (in this case mostly membrane proteins) are fused to an terminal fragment (Nub) and to a C-terminal fragment of ubiquitin (Cub). The two fragments do not associate to fo...
subset: PSI-MI slim
synonym: "ub reconstruction" EXACT PSI-MI-short []
is_a: MI:0228 ! cytoplasmic complementation assay
[Term]
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0803 ! expression level alteration
[Term]
id: MI:0225
name: chromatin immunoprecipitation array
def: "The method combines a modified chromatin immunoprecipitation (ChIP) procedure, with DNA microarray analysis. Cells are fixed with formaldehyde, harvested, and disrupted by sonication. The DNA fragments cross-linked to a protein of interest are ...
subset: PSI-MI slim
synonym: "chip-chip" EXACT PSI-MI-short []
is_a: MI:0008 ! array technology
is_a: MI:0402 ! chromatin immunoprecipitation assay
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0090 ! protein complementation assay
[Term]
id: MI:0229
name: green fluorescence protein complementation assay
def: "Protein-protein interaction trap based on fusions of bait and prey protein to two dissected fragment of GFP. The system implemented in E. coli, allow screening of partners, including membrane proteins and also detect transient interaction that ...
subset: PSI-MI slim
synonym: "gfp complementation" EXACT PSI-MI-short []
is_a: MI:0228 ! cytoplasmic complementation assay
[Term]
scripts/Data/psi-mi.obo view on Meta::CPAN
synonym: "two hybrid pooling" EXACT PSI-MI-short []
is_a: MI:0018 ! two hybrid
[Term]
id: MI:0399
name: two hybrid fragment pooling approach
def: "This two hybrid approach involves the screening of a large number of individual proteins against a comprehensive library of randomly generated fragment as prey. The usage of degenerated fragment allows identification of the minimal protein regi...
subset: PSI-MI slim
synonym: "2h fragment pooling" EXACT PSI-MI-short []
is_a: MI:0398 ! two hybrid pooling approach
[Term]
id: MI:0400
name: affinity technology
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0045 ! experimental interaction detection
[Term]
id: MI:0402
name: chromatin immunoprecipitation assay
def: "Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells. ChIP involves treating cells or tissue briefly with formaldehyde to crosslink prot...
subset: PSI-MI slim
synonym: "ch-ip" EXACT PSI-MI-short []
is_a: MI:0400 ! affinity technology
[Term]
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0195 ! covalent binding
[Term]
id: MI:0409
name: dna footprinting
def: "Experimental method used to identify the region of a nucleic acid involved in an interaction with a protein. One sample of a radiolabeled nucleic acid of known sequence is submitted to partial digestion. A second sample is incubated with its in...
subset: PSI-MI slim
is_obsolete: true
[Term]
id: MI:0410
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0365 ! enzyme tag
[Term]
id: MI:0520
name: ha tag
def: "The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemagglutinin protein) for which antibodies are commercially available." [PMID:14755292]
subset: PSI-MI slim
synonym: "YPYDVPDYA epitope tag" EXACT PSI-MI-alternate []
is_a: MI:0507 ! tag
[Term]
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0507 ! tag
[Term]
id: MI:0522
name: myc tag
def: "The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem." [PMID:14755292]
subset: PSI-MI slim
synonym: "EUKLISEED epitope tag" EXACT PSI-MI-alternate []
is_a: MI:0507 ! tag
[Term]
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0902 ! rna cleavage
[Term]
id: MI:0572
name: dna cleavage
def: "Covalent bond breakage of a DNA molecule leading to the formation of smaller fragments." [PMID:14755292]
subset: PSI-MI slim
is_a: MI:0910 ! nucleic acid cleavage
[Term]
id: MI:0573
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0417 ! footprinting
[Term]
id: MI:0603
name: dimethylsulphate footprinting
def: "Dimethylsulphate (DMS) is the most commonly used chemical to study DNA-protein interactions. DMS induces methylation of guanine residues so DNA interaction with protein binding to AT rich sequences or to the phosphate backbone may be not detect...
subset: PSI-MI slim
synonym: "dms footprinting" EXACT PSI-MI-short []
is_a: MI:0602 ! chemical footprinting
[Term]
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0807 ! comigration in gel electrophoresis
[Term]
id: MI:0809
name: bimolecular fluorescence complementation
def: "The bimolecular fluorescence complementation (BiFC) is an assay for determination of the locations of protein interactions in living cells. This approach is based on complementation between two non fluorescent fragments of the yellow fluorescen...
subset: PSI-MI slim
synonym: "bifc" EXACT PSI-MI-short []
is_a: MI:0051 ! fluorescence technology
is_a: MI:0090 ! protein complementation assay
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0421 ! identification by antibody
[Term]
id: MI:0814
name: protease accessibility laddering
def: "In protease accessibility laddering (PAL) tagged proteins are purified on magnetic beads in their natively folded state. While attached to the beads, proteins are probed with proteases. Proteolytic fragments are eluted and detected by immunobl...
subset: PSI-MI slim
synonym: "pal" EXACT PSI-MI-alternate []
synonym: "protease access" EXACT PSI-MI-short []
is_a: MI:0605 ! enzymatic footprinting
scripts/Data/psi-mi.obo view on Meta::CPAN
subset: PSI-MI slim
is_a: MI:0428 ! imaging technique
[Term]
id: MI:0828
name: polyprotein fragment
def: "Subpart of a polyprotein that is naturally cleaved in vivo." [PMID:14577292]
subset: PSI-MI slim
synonym: "chain" RELATED []
synonym: "polyprotein frag" EXACT PSI-MI-short []
is_a: MI:0252 ! biological feature
[Term]
id: MI:0829
name: multiple parent reference
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0414 ! enzymatic reaction
[Term]
id: MI:0845
name: spin label
def: "Paramagnetic fragment, most often a cyclic nitroxide derivative, covalently attached to a molecule of interest." [PMID:10966640]
subset: PSI-MI slim
is_a: MI:0505 ! experimental feature
[Term]
id: MI:0846
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0013 ! biophysical
[Term]
id: MI:0895
name: protein kinase A complementation
def: "This method uses Renilla luciferase (Rluc)-based protein fragment complementation assay (PCA) that is designed specifically to investigate dynamic protein complexes (association and dissociation). It is chose to generate a PCA based on the Rluc...
subset: PSI-MI slim
synonym: "pka complementation" EXACT PSI-MI-short []
is_a: MI:0228 ! cytoplasmic complementation assay
[Term]
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0048 ! filamentous phage display
[Term]
id: MI:0900
name: p8 filamentous phage display
def: "pVIII is the major coat protein of filamentous phage. Its amino-terminus is exposed to solvent and tolerates the insertion of relatively large peptide fragments. By inserting the peptide coding sequence into the phage copy of the pVIII gene up ...
subset: PSI-MI slim
synonym: "high valency display" EXACT PSI-MI-alternate []
synonym: "p8 filamentous phage" EXACT PSI-MI-short []
is_a: MI:0048 ! filamentous phage display
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0907 ! conformational status
[Term]
id: MI:0910
name: nucleic acid cleavage
def: "Covalent bond breakage of a nucleic acid molecule leading to the formation of smaller fragments." [PMID:14755292]
subset: PSI-MI slim
synonym: "ncl acid cleavage" EXACT PSI-MI-short []
is_a: MI:0194 ! cleavage reaction
[Term]
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0415 ! enzymatic study
[Term]
id: MI:0921
name: surface plasmon resonance array
def: "This array technology allows the screening of binding abilities of hundreds or thousands of biomolecules (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) printed onto the gold-coated chip by using an instrumen...
subset: PSI-MI slim
synonym: "Biacore Flexchip(r)" EXACT PSI-MI-alternate []
synonym: "spr array" EXACT PSI-MI-short []
synonym: "SPRi-Plex " EXACT PSI-MI-alternate []
synonym: "SPRImager" EXACT PSI-MI-alternate []
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0091 ! chromatography technology
[Term]
id: MI:0929
name: nothern blot
def: "A standard procedure to identify RNA fragments containing specific\nsequences. In this procedure RNA fragments are separated by\nelectrophoresis, the fragments are transferred to a membrane and the\nmembrane is incubated with a radio labelled p...
subset: PSI-MI slim
synonym: "northen" EXACT PSI-MI-alternate []
is_a: MI:0078 ! nucleotide sequence identification
[Term]
scripts/Data/psi-mi.obo view on Meta::CPAN
is_a: MI:0472 ! pdbe
[Term]
id: MI:0937
name: glu tag
def: "This peptide is a 314 to 319 amino acids fragment of the middle T antigen of mouse polymavirus. Glu-Glu epitope peptide." [PMID:8077219]
subset: PSI-MI slim
synonym: "glu tag" EXACT PSI-MI-short []
is_a: MI:0507 ! tag
[Term]
Bio-KBase
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lib/Bio/KBase/CDMI/CDMILoader.pm view on Meta::CPAN
my ($ih) = @_;
# Declare the return variables for the ID and comment. When we read a
# header record, we'll set the next-ID variable and that will stop the
# read loop.
my ($nextID, $nextComment);
# This will hold the sequence fragments.
my @lines;
# Loop until we've read the whole sequence.
while (! eof $ih && ! defined $nextID) {
# Read the next line.
my $line = <$ih>;
Bio-Lite
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lib/Bio/Lite.pm view on Meta::CPAN
=head2 pairedEndSeqFileIterator
Open Paired-End Sequence files using seqFileIterator()
Paird-End files are generated by Next Generation Sequencing technologies (like Illumina) where two
reads are sequenced from the same DNA fragment and saved in separated files.
Example:
my $it = pairedEndSeqFileIterator($file);
while (my $entry = $it->()) {
Bio-MAGE
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MAGE/BioSequence/BioSequence.pm view on Meta::CPAN
bless( {
'__SELF' => bless( {
'__NAME' => undef,
'__IS_REF' => 0,
'__CARDINALITY' => '1',
'__DOCUMENTATION' => 'The type of biosequence, i.e. gene, exon, UniGene cluster, fragment, BAC, EST, etc.',
'__CLASS_NAME' => 'BioSequence',
'__RANK' => undef,
'__ORDERED' => undef
}, 'Bio::MAGE::Association::End' ),
'__OTHER' => bless( {
'__NAME' => 'type',
'__IS_REF' => 1,
'__CARDINALITY' => '1',
'__DOCUMENTATION' => 'The type of biosequence, i.e. gene, exon, UniGene cluster, fragment, BAC, EST, etc.',
'__CLASS_NAME' => 'OntologyEntry',
'__RANK' => '4',
'__ORDERED' => 0
}, 'Bio::MAGE::Association::End' )
}, 'Bio::MAGE::Association' ),
MAGE/BioSequence/BioSequence.pm view on Meta::CPAN
Methods for the C<type> association.
From the MAGE-OM documentation:
The type of biosequence, i.e. gene, exon, UniGene cluster, fragment, BAC, EST, etc.
=over
Bio-MAGETAB
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inc/Module/AutoInstall.pm view on Meta::CPAN
return 1;
}
sub postamble {
$PostambleUsed = 1;
my $fragment;
$fragment .= <<"AUTO_INSTALL" if !$InstallDepsTarget;
config :: installdeps
\t\$(NOECHO) \$(NOOP)
AUTO_INSTALL
$fragment .= <<"END_MAKE";
checkdeps ::
\t\$(PERL) $0 --checkdeps
installdeps ::
inc/Module/AutoInstall.pm view on Meta::CPAN
listalldeps ::
\t$PostambleActionsListAllDeps
END_MAKE
return $fragment;
}
1;
__END__
Bio-MLST-Check
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-h Print this message and exit
-v Print version number and exit
```
# Input format
The input files must be in [FASTA format](https://en.wikipedia.org/wiki/FASTA_format) and contain nucleotide sequences. These can be full genome sequences, fragmented _de novo_ assemblies or individual genes. If the gene is truncated or split over 2 ...
# Outputs
## mlst_results.allele.csv
This is a tab separated spreadsheet containing the ST number of each input FASTA file and the corresponding allele numbers for each gene in the scheme. If one of the alleles is not contained in the database, then it will be flagged with 'U' and the 3...
Bio-MUST-Apps-FortyTwo
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lib/Bio/MUST/Apps/FortyTwo/Manual.pod view on Meta::CPAN
parameter of the C<config> file.
The C<BLAST> aligner has been much improved with respect to the aligner of the
original C<forty>. It extracts all the HSPs for the selected template(s) from
the XML C<BLAST> report and uses them as guides for integrating the orthologue
fragments into the MSA. Then, once all fragments have been integrated for all
candidate organisms, it merges them into a single contiguous sequence per
orthologue. When fragments overlap, the merger gives precedence to the fragments
corresponding to the highest-scoring templates and HSPs.
When the new C<exonerate> aligner is preferred, only the longest selected
template is used. In most cases, the orthologue can be aligned as a single large
fragment. If not, C<42> emits different types of warnings depending on the exact
issue. In worst cases (e.g., C<exonerate> crashing), the orthologue cannot be
integrated, often due to structural rearrangements between the orthologue and
the template. To avoid discarding the orthologue in such cases, one can enable
C<BLAST> as a fall-back for exonerate failures by setting the C<aligner>
parameter to C<exoblast>.
lib/Bio/MUST/Apps/FortyTwo/Manual.pod view on Meta::CPAN
parameter C<ali_keep_lengthened_seqs> in the C<config> file.
=head3 C<#NEW#> tags
All newly added orthologues are tagged by a specific C<#NEW#> suffix. This tag
helps C<42> to organize the post-processing of new sequences (e.g., fragment
merging and redundancy detection) but is also useful for the end-user to
identify which sequences have been added by C<42>. Therefore any preexisting
C<#NEW#> tag is cleared when C<42> starts processing a MSA.
While automatic untagging can be disabled via the parameter
Bio-MUST-Apps-HmmCleaner
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lib/Bio/MUST/Apps/HmmCleaner.pm view on Meta::CPAN
my @cleaners;
# arguments for Hmmer driver
my $model_args = {
'--plaplace' => undef,
'--fragthresh' => "0.0",
'--symfrac' => $self->symfrac,
#~ '--wnone' => undef,
};
# arguments for Temporary fasta files
Bio-MUST-Apps-TwoScalp
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bin/two-scalp.pl view on Meta::CPAN
use aliased 'Bio::MUST::Apps::TwoScalp::Profile2Profile';
const my $DEF_FAM => ':default';
# set up mafft options (and pseudo-options --fragments and --long)
my %opt;
$opt{ '--fragments' } = () if $ARGV_fragments;
$opt{ '--long' } = () if $ARGV_long;
$opt{ '--keeplength' } = () if $ARGV_keep_length;
$opt{ '--thread' } = $ARGV_threads if $ARGV_threads > 1;
if ($ARGV_linsi) {
$opt{ '--maxiterate' } = 1000;
bin/two-scalp.pl view on Meta::CPAN
# set up new (expendable) hash to change used options
tie my %reduced_opt, 'Tie::IxHash';
%reduced_opt = %opt;
if ($type eq 'prof') {
delete @reduced_opt{ qw( --fragments --long --keeplength ) };
$new_profile = Profile2Profile->new( file1 => $toalign_file,
file2 => $profile_file,
options => \%reduced_opt );
}
bin/two-scalp.pl view on Meta::CPAN
family) are also present, these are degapped and aligned on the profile
obtained after aligning the specified families.
=for Euclid: family.type: string
=item --fragments
Run MAFFT with the C<--addfragments> option [default: no]. This option should
be specified when the sequences to align are (much) shorter than the sequences
that are already aligned. See
L<https://mafft.cbrc.jp/alignment/server/add.html> for details.
=item --long
Bio-MUST-Core
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lib/Bio/MUST/Core/Ali.pm view on Meta::CPAN
# TREE-FINDER: http://www.treefinder.de/tf-march2011-manual.pdf
# A sequence name may consist of 1 to 10 alphanumeric characters, dashes "-",
# dots ".", underscores "_", or some of "/", "?", "*", "+". No space is
# allowed inside the names. The first name character must be a letter or an
# underscore. A sequence fragment may start behind position 10 after a
# sequence name, or anywhere in a line without a name.
# TREE-PUZZLE [data/globin.a]
# 7 128
# HBB_HUMAN HLTPEEKSAV TALWGKVNVD EVGGEALGRL LVVYPWTQRF FESFDLSMGN
Bio-MUST-Drivers
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bin/annotate-ali.pl view on Meta::CPAN
=for Euclid: file.type: readable
=item --[ref-]regex [=] <regex>
Regular expression for capturing the reference seq id fragment that has to be
used for annotating infile seq ids.
=for Euclid: regex.type: string
=back
Bio-NEXUS
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t/data/compliant/long-names.nex view on Meta::CPAN
#NEXUS
BEGIN TAXA;
dimensions ntax=8;
taxlabels A B C D E F SupercalifragilisticexpialidOTU H;
END;
BEGIN CHARACTERS;
dimensions nchar=5;
charlabels SupercalifragilisticexpialLabel Two Three
Four Five;
format datatype=protein missing=? gap=-;
matrix
A --QNE
B --QNE
C TWO--
D THREE
E FORE-
F FIVE-
SupercalifragilisticexpialidOTU SIX--
H SEVEN;
END;
BEGIN TREES;
tree SupercalifragilisticexpialiTree = (((((((A:1,B:1):1,C:2):1,D:3):1,E:4):1,F:5):1,SupercalifragilisticexpialidOTU:6):1,H:7);
END;
Bio-Phylo
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lib/Bio/Phylo/Parsers/Cdao.pm view on Meta::CPAN
# an ontology using an anchor '#', e.g. in CDAO
if ( $predicate =~ m/^(.+#)(.+?)$/ ) {
( $ns, $term ) = ( $1, $2 );
}
# this is for cases where the term is a path fragment inside a namespace,
# i.e. preceded by a '/', as in dublin core
elsif ( $predicate =~ m/^(.+\/)([^\/]+?)$/ ) {
( $ns, $term ) = ( $1, $2 );
}
Bio-Polloc
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lib/Bio/Polloc/Typing/bandingPattern.pm view on Meta::CPAN
=head2 scan
See L<Bio::Polloc::TypingI-E<gt>scan>.
L<fragments> must be implemented by the C<Bio::Polloc::Typing::bandingPattern::*>
object.
=cut
sub scan {
my ($self, @args) = @_;
my ($locigroup) = $self->_rearrange([qw(LOCIGROUP)], @args);
$locigroup ||= $self->locigroup;
return $self->_scan_locigroup($self->fragments(-locigroup=>$locigroup));
}
=head2 cluster
=head2 typing_value
lib/Bio/Polloc/Typing/bandingPattern.pm view on Meta::CPAN
}
=head1 SPECIFIC METHODS
=head2 fragments
Generates fragments.
=head3 Arguments
=over
lib/Bio/Polloc/Typing/bandingPattern.pm view on Meta::CPAN
=back
=head3 Returns
A L<Bio::Polloc::LociGrop>, where each locus is a fragment.
=head3 Throws
A L<Bio::Polloc::Polloc::NotImplementedException> unless implemented
by the specific C<Bio::Polloc::Typing::bandingPattern::*> object.
=cut
sub fragments { $_[0]->throw("fragments", $_[0], "Bio::Polloc::Polloc::NotImplementedException") }
=head2 max_size
Gets/sets the maximum locus size. No limit (C<inf>) by default.
Bio-Procedural
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t/data/amino.fa view on Meta::CPAN
>CYS1_DICDI fragment
SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE
>ALEU_HORVU
MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGK
SYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRD
( run in 1.714 second using v1.01-cache-2.11-cpan-b16cb0d3907 )