/ 
GBrowse-2.56
River stage zero No dependents
/ Bio::Graphics::Browser2::Plugin::Aligner

NAME

Bio::Graphics::Browser2::Plugin::Aligner - Dump multiple alignments from GBrowse

SYNOPSIS

In the appropriate gbrowse configuration file:

plugins = Aligner

# and later
[Aligner:plugin]
alignable_tracks   = EST
upcase_tracks      = CDS Motifs
upcase_default     = CDS

DESCRIPTION

The Aligner plugin dumps multiple nucleotide-to-nucleotide alignments in text form. For it to work properly, the genomic DNA must be loaded, as well as the DNAs for each of the aligned objects. In addition, the GFF load file must represent both the source and the target of the alignment using the Target notation. For example:

ctgA  est  match  1050  3202  .  +  .  Target EST:agt830.5 1 554
ctgA  est  HSP    1050  1500  .  +  .  Target EST:agt830.5 1 451
ctgA  est  HSP    3000  3202  .  +  .  Target EST:agt830.5 452 654

OPTIONS

The following options are recognized. They must be placed into a configuration file section named [Aligner:plugin].

Option             Description

alignable_tracks   Space-delimited list of tracks to include in
                   the multiple alignment. The genome is always
                   included. If this option is not present, then
                   gbrowse will automatically include any track
                   that has the "draw_target" option set.

upcase_tracks      Space-delimited list of tracks that will be used
                   to UPCASE the genomic DNA. This is very useful if
                   you want to embed the positions of coding regions
                   or other features inside the multiple alignment.
                   Uppercasing will not be turned on by default. The
                   user must press the "Configure" button, and select
                   which of the uppercase tracks are to be activated
                   from a radiolist.
upcase_default     A space-delimited list of tracks that will be uppercased
                   by default.


ragged_default     A small integer indicating that the aligner should
                   include some unaligned bases from the end of each sequence.
                   This is useful for seeing the sequencing primer or cloning
                   site in ESTs.

BUGS

None known yet.

SEE ALSO

Bio::Graphics::Browser2::Plugin

AUTHOR

Lincoln Stein <lstein@cshl.org>.

Copyright (c) 2001 Cold Spring Harbor Laboratory.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.