BioPerl
view release on metacpan or search on metacpan
=item * Scott Cain <scott at scottcain.net> - Bio::Graphics::Glyph, Bio::DB::GFF::Adaptor::dbi::pg, GFF related tools and scripts
=item * Yee Man Chan <ymc at yahoo.com> - Bio::Tools::dpAlign
=item * Brad Chapman <chapmanb at arches.uga.edu>
=item * Roy R. Chaudhuri <roy.chaudhuri at gmail.com> - Bio::SeqUtils Bio::Align::Utilities
=item * Michele Clamp <michele at sanger.ac.uk>
=item * Malcolm Cook <mec at stowers-institute.org>
=item * Tony Cox <avc at sanger.ac.uk>
=item * James Cuff <james at sanger.ac.uk>
=item * Andrew Dalke <dalke at acm.org>
=item * Allen Day <allenday at ucla.edu>
=item * Jared Fox <jaredfox at ucla.edu> - Bio::SeqIO::interpro
Bio/RangeI.pm view on Meta::CPAN
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Heikki Lehvaslaiho
Email: heikki-at-bioperl-dot-org
=head1 CONTRIBUTORS
Juha Muilu (muilu@ebi.ac.uk)
Sendu Bala (bix@sendu.me.uk)
Malcolm Cook (mec@stowers-institute.org)
Stephen Montgomery (sm8 at sanger.ac.uk)
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::RangeI;
Bio/SearchIO/Writer/HTMLResultWriter.pm view on Meta::CPAN
}
} elsif( $result->algorithm =~ /FAST/i ) {
return $result->algorithm . " " . $result->algorithm_version . "<br>" .
"\n<b>Reference:</b> Pearson et al, Genomics (1997) 46:24-36<p>";
} else {
return '';
}
}
# from Perl Cookbook 2.17
sub _numwithcommas {
my $num = reverse( $_[0] );
$num =~ s/(\d{3})(?=\d)(?!\d*\.)/$1,/g;
return scalar reverse $num;
}
=head2 Methods Bio::SearchIO::SearchWriterI
L<Bio::SearchIO::SearchWriterI> inherited methods.
Bio/SearchIO/Writer/TextResultWriter.pm view on Meta::CPAN
};
}
} elsif( $result->algorithm =~ /FAST/i ) {
return $result->algorithm. " ". $result->algorithm_version . "\n".
"\nReference: Pearson et al, Genomics (1997) 46:24-36\n";
} else {
return '';
}
}
# from Perl Cookbook 2.17
sub _numwithcommas {
my $num = reverse( $_[0] );
$num =~ s/(\d{3})(?=\d)(?!\d*\.)/$1,/g;
return scalar reverse $num;
}
sub _linewrap {
my ($str) = @_;
if($TextWrapLoaded) {
return Text::Wrap::wrap("","",$str); # use Text::Wrap
Bio/SeqIO/lasergene.pm view on Meta::CPAN
#-----------------------------------------5~------------------------------------
# PACKAGE : Bio::SeqIO::lasergene
# AUTHOR : Malcolm Cook <mec@stowers-institute.org>
# CREATED : Feb 16 1999
#
# _History_
#
# This code is based on the Bio::SeqIO::raw module with
# the necessary minor tweaks necessary to get it to read (only)
# Lasergene formatted sequences
#
# Cleaned up by Torsten Seemann June 2006
Bio/SeqIO/lasergene.pm view on Meta::CPAN
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHORS
Torsten Seemann - torsten.seemann AT infotech.monash.edu.au
Malcolm Cook - mec AT stowers-institute.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
Bio/SeqIO/strider.pm view on Meta::CPAN
# BioPerl module for Bio::SeqIO::strider
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Malcolm Cook <mec@stowers-institute.org>
#
# You may distribute this module under the same terms as perl itself
#
# _history
# April 7th, 2005 Malcolm Cook authored
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqIO::strider - DNA strider sequence input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class.
Bio/SeqIO/strider.pm view on Meta::CPAN
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHORS - Malcolm Cook
Email: mec@stowers-institute.org
=head1 CONTRIBUTORS
Modelled after Bio::SeqIO::fasta by Ewan Birney E<lt>birney@ebi.ac.ukE<gt> and
Lincoln Stein E<lt>lstein@cshl.orgE<gt>
=head1 APPENDIX
Bio/Tools/GFF.pm view on Meta::CPAN
=head1 AUTHOR - Matthew Pocock
Email mrp-at-sanger.ac.uk
=head1 CONTRIBUTORS
Jason Stajich, jason-at-biperl-dot-org
Chris Mungall, cjm-at-fruitfly-dot-org
Steffen Grossmann [SG], grossman at molgen.mpg.de
Malcolm Cook, mec-at-stowers-institute.org
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::GFF;
* [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
* [2928] - GuessSeqFormat raw [maj]
* [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
* [2922] - open() directive issue [cjfields]
* [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
* [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
* [2899] - SeqFeature::Store host issues [lstein, dbolser]
* [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
cjfields]
* [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
* [2876] - CDD search with RemoteBlast [Malcolm Cook]
* [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
* [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
* [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
* [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
* [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
* [2758] - Bio::AssemblyIO ace problems [fangly]
* [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
* [2726] - ace file IO [Josh, fangly]
* [2700] - Refactor Build.PL [cjfields]
* [2673] - addition of simple Root-based clone() method [cjfields]
o New Alignment IO framework
o New Index modules (Swissprot)
o New modules for running Blast within perl
(Bio::Tools::Run::StandAloneBlast). Added modules for running
Multiple Sequence Alignment tools ClustalW and TCoffee
(Bio::Tools::Run::Alignment).
o New Cookbook-style tutorial (see bptutorial.pl). Improved
documentation across the package.
o Much improved cross platform support. Many known incompatibilities
have been fixed; however, NT and Mac do not work across the entire
setup (see PLATFORMS).
o Many bug fixes, code restructuring, etc. Overall stability and
maintainability benefit a lot.
o A total of 957 automatic tests
maintenance/big_split/file_classification.csv view on Meta::CPAN
,"Bio/Tools/EUtilities/Summary/DocSum.pm"
,"Bio/Tools/EUtilities/Summary/ItemContainerI.pm"
,"Bio/Tools/EUtilities/Summary/Item.pm"
,"Bio/Tools/EUtilities/Info/LinkInfo.pm"
,"Bio/Tools/EUtilities/Info/FieldInfo.pm"
,"Bio/Tools/EUtilities/HistoryI.pm"
,"Bio/Tools/EUtilities/Info.pm"
,"Bio/Tools/EUtilities/EUtilParameters.pm"
,"Bio/Tools/EUtilities/EUtilDataI.pm"
,"Bio/Tools/EUtilities/History.pm"
,"Bio/Tools/EUtilities/Cookie.pm"
,"Bio/Tools/EUtilities/Link.pm"
,"Bio/Tools/EUtilities/Summary.pm"
,"Bio/Tools/EUtilities/Query/GlobalQuery.pm"
,"Bio/Tools/EUtilities/Query.pm"
,"Bio/Tools/EUtilities/Link/LinkSet.pm"
,"Bio/Tools/EUtilities/Link/UrlLink.pm"
,"Bio/Tools/FootPrinter.pm"
,"Bio/Tools/TandemRepeatsFinder.pm"
,"Bio/Tools/Analysis/SimpleAnalysisBase.pm"
,"Bio/Tools/Analysis/DNA/ESEfinder.pm"
t/data/NC_000007-ribosomal-slippage.gb view on Meta::CPAN
Fewell,G.A., Delehaunty,K.D., Miner,T.L., Nash,W.E., Cordes,M.,
Du,H., Sun,H., Edwards,J., Bradshaw-Cordum,H., Ali,J., Andrews,S.,
Isak,A., Vanbrunt,A., Nguyen,C., Du,F., Lamar,B., Courtney,L.,
Kalicki,J., Ozersky,P., Bielicki,L., Scott,K., Holmes,A.,
Harkins,R., Harris,A., Strong,C.M., Hou,S., Tomlinson,C.,
Dauphin-Kohlberg,S., Kozlowicz-Reilly,A., Leonard,S., Rohlfing,T.,
Rock,S.M., Tin-Wollam,A.M., Abbott,A., Minx,P., Maupin,R.,
Strowmatt,C., Latreille,P., Miller,N., Johnson,D., Murray,J.,
Woessner,J.P., Wendl,M.C., Yang,S.P., Schultz,B.R., Wallis,J.W.,
Spieth,J., Bieri,T.A., Nelson,J.O., Berkowicz,N., Wohldmann,P.E.,
Cook,L.L., Hickenbotham,M.T., Eldred,J., Williams,D., Bedell,J.A.,
Mardis,E.R., Clifton,S.W., Chissoe,S.L., Marra,M.A., Raymond,C.,
Haugen,E., Gillett,W., Zhou,Y., James,R., Phelps,K., Iadanoto,S.,
Bubb,K., Simms,E., Levy,R., Clendenning,J., Kaul,R., Kent,W.J.,
Furey,T.S., Baertsch,R.A., Brent,M.R., Keibler,E., Flicek,P.,
Bork,P., Suyama,M., Bailey,J.A., Portnoy,M.E., Torrents,D.,
Chinwalla,A.T., Gish,W.R., Eddy,S.R., McPherson,J.D., Olson,M.V.,
Eichler,E.E., Green,E.D., Waterston,R.H. and Wilson,R.K.
TITLE The DNA sequence of human chromosome 7
JOURNAL Nature 424 (6945), 157-164 (2003)
PUBMED 12853948
t/data/NC_000007-ribosomal-slippage.gb view on Meta::CPAN
Santos,R., Sheridan,A., Sougnez,C., Stange-Thomann,N.,
Stojanovic,N., Subramanian,A., Wyman,D., Rogers,J., Sulston,J.,
Ainscough,R., Beck,S., Bentley,D., Burton,J., Clee,C., Carter,N.,
Coulson,A., Deadman,R., Deloukas,P., Dunham,A., Dunham,I.,
Durbin,R., French,L., Grafham,D., Gregory,S., Hubbard,T.,
Humphray,S., Hunt,A., Jones,M., Lloyd,C., McMurray,A., Matthews,L.,
Mercer,S., Milne,S., Mullikin,J.C., Mungall,A., Plumb,R., Ross,M.,
Shownkeen,R., Sims,S., Waterston,R.H., Wilson,R.K., Hillier,L.W.,
McPherson,J.D., Marra,M.A., Mardis,E.R., Fulton,L.A.,
Chinwalla,A.T., Pepin,K.H., Gish,W.R., Chissoe,S.L., Wendl,M.C.,
Delehaunty,K.D., Miner,T.L., Delehaunty,A., Kramer,J.B., Cook,L.L.,
Fulton,R.S., Johnson,D.L., Minx,P.J., Clifton,S.W., Hawkins,T.,
Branscomb,E., Predki,P., Richardson,P., Wenning,S., Slezak,T.,
Doggett,N., Cheng,J.F., Olsen,A., Lucas,S., Elkin,C.,
Uberbacher,E., Frazier,M., Gibbs,R.A., Muzny,D.M., Scherer,S.E.,
Bouck,J.B., Sodergren,E.J., Worley,K.C., Rives,C.M., Gorrell,J.H.,
Metzker,M.L., Naylor,S.L., Kucherlapati,R.S., Nelson,D.L.,
Weinstock,G.M., Sakaki,Y., Fujiyama,A., Hattori,M., Yada,T.,
Toyoda,A., Itoh,T., Kawagoe,C., Watanabe,H., Totoki,Y., Taylor,T.,
Weissenbach,J., Heilig,R., Saurin,W., Artiguenave,F., Brottier,P.,
Bruls,T., Pelletier,E., Robert,C., Wincker,P., Smith,D.R.,
t/data/calm.swiss view on Meta::CPAN
RL Nat. Struct. Biol. 8:990-997(2001).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS).
RX PubMed=1474585;
RA Chattopadhyaya R., Meador W.E., Means A.R., Quiocho F.A.;
RT "Calmodulin structure refined at 1.7 A resolution.";
RL J. Mol. Biol. 228:1177-1192(1992).
RN [14]
RP X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS).
RX PubMed=7803388;
RA Cook W.J., Walter L.J., Walter M.R.;
RT "Drug binding by calmodulin: crystal structure of a calmodulin-
RT trifluoperazine complex.";
RL Biochemistry 33:15259-15265(1994).
RN [15]
RP X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) OF 5-148.
RX MEDLINE=21666515; PubMed=11807546; DOI=10.1038/415396a;
RA Drum C.L., Yan S.-Z., Bard J., Shen Y.Q., Lu D., Soelaiman S.,
RA Grabarek Z., Bohm A., Tang W.-J.;
RT "Structural basis for the activation of anthrax adenylyl cyclase
RT exotoxin by calmodulin.";
t/data/interpro_relationship.xml view on Meta::CPAN
<pub_list>
<publication id="PUB00010722">
<author_list>Griffiths L, Stratford IJ.</author_list>
<title>Platelet-derived endothelial cell growth factor thymidine phosphorylase in tumour growth and response to therapy.</title>
<db_xref db="PUBMED" dbkey="9310231"/>
<journal>Br. J. Cancer</journal>
<location issue="6" pages="689-93" volume="76"/>
<year>1997</year>
</publication>
<publication id="PUB00010723">
<author_list>Pugmire MJ, Cook WJ, Jasanoff A, Walter MR, Ealick SE.</author_list>
<title>Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase.</title>
<db_xref db="PUBMED" dbkey="9698549"/>
<journal>J. Mol. Biol.</journal>
<location issue="2" pages="285-99" volume="281"/>
<year>1998</year>
</publication>
<publication id="PUB00010724">
<author_list>Pugmire MJ, Ealick SE.</author_list>
<title>The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation.</title>
<db_xref db="PUBMED" dbkey="9817849"/>
t/data/ribosome-slippage.gb view on Meta::CPAN
Santos,R., Sheridan,A., Sougnez,C., Stange-Thomann,N.,
Stojanovic,N., Subramanian,A., Wyman,D., Rogers,J., Sulston,J.,
Ainscough,R., Beck,S., Bentley,D., Burton,J., Clee,C., Carter,N.,
Coulson,A., Deadman,R., Deloukas,P., Dunham,A., Dunham,I.,
Durbin,R., French,L., Grafham,D., Gregory,S., Hubbard,T.,
Humphray,S., Hunt,A., Jones,M., Lloyd,C., McMurray,A., Matthews,L.,
Mercer,S., Milne,S., Mullikin,J.C., Mungall,A., Plumb,R., Ross,M.,
Shownkeen,R., Sims,S., Waterston,R.H., Wilson,R.K., Hillier,L.W.,
McPherson,J.D., Marra,M.A., Mardis,E.R., Fulton,L.A.,
Chinwalla,A.T., Pepin,K.H., Gish,W.R., Chissoe,S.L., Wendl,M.C.,
Delehaunty,K.D., Miner,T.L., Delehaunty,A., Kramer,J.B., Cook,L.L.,
Fulton,R.S., Johnson,D.L., Minx,P.J., Clifton,S.W., Hawkins,T.,
Branscomb,E., Predki,P., Richardson,P., Wenning,S., Slezak,T.,
Doggett,N., Cheng,J.F., Olsen,A., Lucas,S., Elkin,C.,
Uberbacher,E., Frazier,M., Gibbs,R.A., Muzny,D.M., Scherer,S.E.,
Bouck,J.B., Sodergren,E.J., Worley,K.C., Rives,C.M., Gorrell,J.H.,
Metzker,M.L., Naylor,S.L., Kucherlapati,R.S., Nelson,D.L.,
Weinstock,G.M., Sakaki,Y., Fujiyama,A., Hattori,M., Yada,T.,
Toyoda,A., Itoh,T., Kawagoe,C., Watanabe,H., Totoki,Y., Taylor,T.,
Weissenbach,J., Heilig,R., Saurin,W., Artiguenave,F., Brottier,P.,
Bruls,T., Pelletier,E., Robert,C., Wincker,P., Smith,D.R.,
t/data/sequencefamily.dat view on Meta::CPAN
RA Jennissen H.P.;
RT "Modulation of calmodulin function by ubiquitin-calmodulin ligase and
RT identification of the responsible ubiquitylation site in vertebrate
RT calmodulin.";
RL Eur. J. Biochem. 255:422-431(1998).
RN [30]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
RC SPECIES=Rat;
RX MEDLINE=85188323; PubMed=3990807;
RA Babu Y.S., Sack J.S., Greenhough T.J., Bugg C.E., Means A.R.,
RA Cook W.J.;
RT "Three-dimensional structure of calmodulin.";
RL Nature 315:37-40(1985).
RN [31]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
RC SPECIES=Rat;
RX MEDLINE=89110997; PubMed=3145979;
RA Babu Y.S., Bugg C.E., Cook W.J.;
RT "Structure of calmodulin refined at 2.2-A resolution.";
RL J. Mol. Biol. 204:191-204(1988).
RN [32]
RP X-RAY CRYSTALLOGRAPHY (2 ANGSTROMS).
RC SPECIES=Bovine;
RX MEDLINE=98104088; PubMed=9438860;
RA Wall M.E., Clarage J.B., Phillips G.N.;
RT "Motions of calmodulin characterized using both Bragg and diffuse
RT X-ray scattering.";
RL Structure 5:1599-1612(1997).
t/data/swiss.dat view on Meta::CPAN
RA Jennissen H.P.;
RT "Modulation of calmodulin function by ubiquitin-calmodulin ligase and
RT identification of the responsible ubiquitylation site in vertebrate
RT calmodulin.";
RL Eur. J. Biochem. 255:422-431(1998).
RN [30]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
RC SPECIES=Rat;
RX MEDLINE=85188323; PubMed=3990807;
RA Babu Y.S., Sack J.S., Greenhough T.J., Bugg C.E., Means A.R.,
RA Cook W.J.;
RT "Three-dimensional structure of calmodulin.";
RL Nature 315:37-40(1985).
RN [31]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
RC SPECIES=Rat;
RX MEDLINE=89110997; PubMed=3145979;
RA Babu Y.S., Bugg C.E., Cook W.J.;
RT "Structure of calmodulin refined at 2.2-A resolution.";
RL J. Mol. Biol. 204:191-204(1988).
RN [32]
RP X-RAY CRYSTALLOGRAPHY (2 ANGSTROMS).
RC SPECIES=Bovine;
RX MEDLINE=98104088; PubMed=9438860;
RA Wall M.E., Clarage J.B., Phillips G.N.;
RT "Motions of calmodulin characterized using both Bragg and diffuse
RT X-ray scattering.";
RL Structure 5:1599-1612(1997).
t/data/withrefm.906 view on Meta::CPAN
<7>
<8>Hiraoka, N., Kita, K., Nakajima, H., Kimizuka, F., Obayashi, A., (1985) J. Ferment. Technol., vol. 63, pp. 151-157.
<1>HaeI
<2>
<3>WGG^CCW
<4>
<5>Haemophilus aegyptius
<6>ATCC 11116
<7>
<8>Murray, K., Morrison, A., Cooke, H.W., Roberts, R.J., Unpublished observations.
<1>HaeII
<2>AccB2I,BfoI,Bme142I,BsmHI,Bsp143II,Bst16I,Bst1473II,BstH2I,Btu34II,HinHI,LpnI,NgoAI,NgoBI,NgoCI,NgoGI,NgoJI,NgoMI,NgoWI
<3>RGCGC^Y
<4>?(5)
<5>Haemophilus aegyptius
<6>ATCC 11116
<7>JKNORW
<8>Lunnen, K.D., Barsomian, J.M., Camp, R.R., Card, C.O., Chen, S.-Z., Croft, R., Looney, M.C., Meda, M.M., Moran, L.S., Nwankwo, D.O., Slatko, B.E., Van Cott, E.M., Wilson, G.G., (1988) Gene, vol. 74, pp. 25-32.
Roberts, R.J., Breitmeyer, J.B., Tabachnik, N.F., Myers, P.A., (1975) J. Mol. Biol., vol. 91, pp. 121-123.
( run in 0.835 second using v1.01-cache-2.11-cpan-e9199f4ba4c )