use Bio::Graphics::Browser2::Realign 'align';
my ($top,$middle,$bottom) = align('gattttttc','gattttccc');
print join "\n",$top,$middle,$bottom,"\n";
DESCRIPTIONThis is a helper utility used by gbrowse to produce global alignments. It uses slow Smith-Waterman, so is only appropriate for short segments that are mostly aligned already.
It can be speeded up significantly by compiling Bio::Graphics::Browser2::CAlign, an XS extension. To do this, build gbrowse with the DO_XS=1 option:
cd Generic-Genome-Browser perl Makefile.PL DO_XS=1
- $aligner = Bio::Graphics::Browser2::Realign->new($src,$target [,\%matrix])
The new() method takes two the two sequence strings to be aligned and
an optional weight matrix. Legal weight matrix keys and their default
values are shown here:
Key name Default Description -------- ------- ----------- match 1 Award one point for an exact match. mismatch -1 Penalize one point for a mismatch. wildcard_match 0 No penalty for a match to a wildcard (e.g. "n"). gap -1 Penalize one point to create a gap. gap_extend 0 No penalty for extending an existing gap. wildcard 'N' The wildcard character.
The alignment algorithm is run when new() is called.
- $score = $aligner->score
- Return the score from the alignment.
- $start = $aligner->start
- Return the start of the aligned region, in source sequence coordinates.
- $end = $aligner->end
- Return the end of the aligned region, in source sequence coordinates.
- $arrayref = $aligner->alignment
Return an arrayref representing the alignment. The array will be
exactly as long as the source sequence. Its indexes correspond to
positions on the source sequence, and its values correspond to
positions on the target sequence. An unaligned base is indicated as
undef. Indexes are zero-based.
For example, this alignment:
gatttttt--c |||||| | gatttt--ccc
corresponds to this arrayref:
index value 0[g] 0[g] 1[a] 1[a] 2[t] 2[t] 3[t] 3[t] 4[t] 4[t] 5[t] 5[t] 6[t] undef 7[t] undef 8[c] 8[c]
- ($top,$middle,$bottom) = $aligner->pads
Returns the alignment as three padded strings indicating the top,
middle and bottom lines of a pretty-printed representation.
print join "\n",$aligner->pads;
Will produce this output:
gatttttt--c |||||| | gatttt--ccc
EXPORTED METHODSNo functions are exported by default, but the following two methods can be imported explicitly.
- ($top,$middle,$bottom) = align($source,$target [,\%matrix])
Align the source and target sequences and return the padded strings
representing the alignment. It is exactly equivalent to calling:
- $segs_arrayref = align_segs($source,$target [,\%matrix])
The align_segs() function aligns $source and $target and returns an
array of non-gapped segments. Each element of the array corresponds
to a contiguous nongapped alignment in the format
This is useful for converting a gapped alignment into a series of nongapped alignments.
In a list context this function will return a list of non-gapped segments.
- $segs_arrayref = Bio::Graphics::Browser2::Realign->pads_to_segments($seq1,$pads,$seq2)
This class method takes two padded sequence strings and the alignment
string that relates them and returns an array ref of non-gapped aligned
sequence in the format:
The 3 strings look like this CA-ACCCCCTTGCAACAACCTTGAGAACCCCAGGGA
AUTHORLincoln Stein <[email protected]>.
Copyright (c) 2003 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.