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.\" ========================================================================
.\"
.IX Title "Bio::Graphics::Browser2::Realign 3pm"
.TH Bio::Graphics::Browser2::Realign 3pm "2018-10-03" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.if n .ad l
.nh
.SH "NAME"
Bio::Graphics::Browser2::Realign \- Perl extension for Smith\-Waterman alignments
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\&  use Bio::Graphics::Browser2::Realign \*(Aqalign\*(Aq;
\&  my ($top,$middle,$bottom) = align(\*(Aqgattttttc\*(Aq,\*(Aqgattttccc\*(Aq);
\&  print join "\en",$top,$middle,$bottom,"\en";
\&
\&  # produces:
\&  gatttttt\-\-c
\&  ||||||    |
\&  gatttt\-\-ccc
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This 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.
.PP
It can be speeded up significantly by compiling
Bio::Graphics::Browser2::CAlign, an \s-1XS\s0 extension.  To do this, build
gbrowse with the DO_XS=1 option:
.PP
.Vb 2
\&  cd Generic\-Genome\-Browser
\&  perl Makefile.PL DO_XS=1
.Ve
.SS "\s-1METHODS\s0"
.IX Subsection "METHODS"
.ie n .IP "$aligner = Bio::Graphics::Browser2::Realign\->new($src,$target [,\e%matrix])" 4
.el .IP "\f(CW$aligner\fR = Bio::Graphics::Browser2::Realign\->new($src,$target [,\e%matrix])" 4
.IX Item "$aligner = Bio::Graphics::Browser2::Realign->new($src,$target [,%matrix])"
The \fInew()\fR method takes two the two sequence strings to be aligned and
an optional weight matrix.  Legal weight matrix keys and their default
values are shown here:
.Sp
.Vb 2
\&   Key name       Default       Description
\&   \-\-\-\-\-\-\-\-       \-\-\-\-\-\-\-       \-\-\-\-\-\-\-\-\-\-\-
\&
\&   match            1           Award one point for an exact match.
\&   mismatch        \-1           Penalize one point for a mismatch.
\&   wildcard_match   0           No penalty for a match to a wildcard (e.g. "n").
\&   gap             \-1           Penalize one point to create a gap.
\&   gap_extend       0           No penalty for extending an existing gap.
\&   wildcard         \*(AqN\*(Aq         The wildcard character.
.Ve
.Sp
The alignment algorithm is run when \fInew()\fR is called.
.ie n .IP "$score = $aligner\->score" 4
.el .IP "\f(CW$score\fR = \f(CW$aligner\fR\->score" 4
.IX Item "$score = $aligner->score"
Return the score from the alignment.
.ie n .IP "$start = $aligner\->start" 4
.el .IP "\f(CW$start\fR = \f(CW$aligner\fR\->start" 4
.IX Item "$start = $aligner->start"
Return the start of the aligned region, in source sequence
coordinates.
.ie n .IP "$end = $aligner\->end" 4
.el .IP "\f(CW$end\fR = \f(CW$aligner\fR\->end" 4
.IX Item "$end = $aligner->end"
Return the end of the aligned region, in source sequence
coordinates.
.ie n .IP "$arrayref = $aligner\->alignment" 4
.el .IP "\f(CW$arrayref\fR = \f(CW$aligner\fR\->alignment" 4
.IX Item "$arrayref = $aligner->alignment"
Return an arrayref representing the alignment.  The array will be
exactly as long as the source sequence.  Its indexes correspond to
positions on the source sequence, and its values correspond to
positions on the target sequence.  An unaligned base is indicated as
undef.  Indexes are zero-based.
.Sp
For example, this alignment:
.Sp
.Vb 3
\&  gatttttt\-\-c
\&  ||||||    |
\&  gatttt\-\-ccc
.Ve
.Sp
corresponds to this arrayref:
.Sp
.Vb 10
\&   index    value
\&   0[g]    0[g]
\&   1[a]    1[a]
\&   2[t]    2[t]
\&   3[t]    3[t]
\&   4[t]    4[t]
\&   5[t]    5[t]
\&   6[t]    undef
\&   7[t]    undef
\&   8[c]    8[c]
.Ve
.ie n .IP "($top,$middle,$bottom) = $aligner\->pads" 4
.el .IP "($top,$middle,$bottom) = \f(CW$aligner\fR\->pads" 4
.IX Item "($top,$middle,$bottom) = $aligner->pads"
Returns the alignment as three padded strings indicating the top,
middle and bottom lines of a pretty-printed representation.
.Sp
For example:
.Sp
.Vb 1
\&  print join "\en",$aligner\->pads;
.Ve
.Sp
Will produce this output:
.Sp
.Vb 3
\&  gatttttt\-\-c
\&  ||||||    |
\&  gatttt\-\-ccc
.Ve
.SS "\s-1EXPORTED METHODS\s0"
.IX Subsection "EXPORTED METHODS"
No functions are exported by default, but the following two methods
can be imported explicitly.
.IP "($top,$middle,$bottom) = align($source,$target [,\e%matrix])" 4
.IX Item "($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:
.Sp
.Vb 1
\&  Bio::Graphics::Browser2::Realign\->new($source,$target)\->pads;
.Ve
.ie n .IP "$segs_arrayref = align_segs($source,$target [,\e%matrix])" 4
.el .IP "\f(CW$segs_arrayref\fR = align_segs($source,$target [,\e%matrix])" 4
.IX Item "$segs_arrayref = align_segs($source,$target [,%matrix])"
The \fIalign_segs()\fR function aligns \f(CW$source\fR and \f(CW$target\fR and returns an
array of non-gapped segments.  Each element of the array corresponds
to a contiguous nongapped alignment in the format
[src_start,src_end,tgt_start,tgt_end].
.Sp
This is useful for converting a gapped alignment into a series of
nongapped alignments.
.Sp
In a list context this function will return a list of non-gapped
segments.
.ie n .IP "$segs_arrayref = Bio::Graphics::Browser2::Realign\->pads_to_segments($seq1,$pads,$seq2)" 4
.el .IP "\f(CW$segs_arrayref\fR = Bio::Graphics::Browser2::Realign\->pads_to_segments($seq1,$pads,$seq2)" 4
.IX Item "$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:
.Sp
.Vb 1
\&  [src_start,src_end,tgt_start,tgt_end]
.Ve
.Sp
The 3 strings look like this CA-ACCCCCTTGCAACAACCTTGAGAACCCCAGGGA
                             | |||||||||||||||||||||||||||||||||
                             \s-1AAGACCCCCTTGCAACAACCTTGAGAACCCCAGGGA\s0
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein <lstein@cshl.org>.
.PP
Copyright (c) 2003 Cold Spring Harbor Laboratory
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See \s-1DISCLAIMER\s0.txt for
disclaimers of warranty.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::Graphics::Browser.