Bio::Graphics::Browser2::Plugin::Aligner - Dump multiple alignments from GBrowse
In the appropriate gbrowse configuration file:
plugins = Aligner # and later [Aligner:plugin] alignable_tracks = EST upcase_tracks = CDS Motifs upcase_default = CDS
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
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.
None known yet.
Lincoln Stein <firstname.lastname@example.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.