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lib/Algorithm/NeedlemanWunsch.pm  view on Meta::CPAN

                | |   |
  sequence B: - t g a t

or

  sequence A: - - a t c t
                  | |
  sequence B: t g a t - -

(and exponentially many other ways, of course). Note that
Needleman-Wunsch considers I<global> alignments, over the entire
length of both sequences; each item is either aligned with an item of
the other sequence, or corresponds to a I<gap> (which is always
aligned with an item - aligning two gaps wouldn't help anything). This
approach is especially suitable for comparing sequences of comparable
length and somewhat similar along their whole lengths - that is,
without long stretches that have nothing to do with each other. If
your sequences don't satisfy these requirements, consider using local
alignment, which, strictly speaking, isn't Needleman-Wunsch, but is
similar enough to be implemented in this module as well - see below
for details.

lib/Algorithm/NeedlemanWunsch.pm  view on Meta::CPAN

charge the gap penalty for gaps at the beginning (i.e. before the
first item) and end (after the last item) of the second sequence
passed to C<align>, so that for example the optimal (with identity
matrix as similarity matrix and a negative gap penalty) alignment of
C<a b c d e f g h> and C<b c h> becomes

  sequence A: a b c d e f g h
                | |
  sequence B:   b c h

instead of the global

  sequence A: a b c d e f g h
                | |         |
  sequence B: - b c - - - - h

Note that local alignment is asymmetrical - when using it, the longer
sequence should be the first passed to
C<Algorithm::NeedlemanWunsch::align>.

=head3 gap_open_penalty, gap_extend_penalty