Difference between revisions of "GBrowse syn Scripts"
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| − | [http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/bin/gbrowse_syn/clustal2hit.pl] is a | + | <span class=pops>[http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/bin/gbrowse_syn/clustal2hit.pl clustal2hit.pl] is a CLUSTALW format alignment data parser. |
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Revision as of 15:10, 5 December 2009
This page describes helper scripts for processing alignment data for loading into GBrowse_syn.
Contents
Parsing Multiple Sequence Alignment Data
The scripts in this section process multiple sequence alignment data in various formats and convert them to the tab-delimited format used to load the GBRowse_syn database.
aln2hit.pl
aln2hit.pl is a generic alignment data parser that reads alignment data into the GBrowse_syn database loading format.
- Purpose
- Use this script in cases where you have a single alignment file and want to convert it to the tab-delimited format that is used to load the GBrowse_syn alignment database.
Example:
perl aln2hit -f clustalw -i my_alignments.aln >my_alignments.txt
| argument | default | description |
|---|---|---|
| f | clustalw | Specifies the alignment file format. MOst common formats recongnized by BioPerl's AlignIO parsers are supported. Use clustalw or fasta for best results. |
| i | Specifies the name of the input alignment file |
clustal2hit.pl
clustal2hit.pl is a CLUSTALW format alignment data parser.
| argument | default | description |
|---|---|---|
mercatoraln_to_synhits.pl
| argument | default | description |
|---|---|---|
Direct Database Loading Scripts
The scripts in this section load data from multiple sequence alignment files into the GBrowse_syn alignment database
load_alignment_database.pl
| argument | default | description |
|---|---|---|
load_alignments_gff3.pl
| argument | default | description |
|---|---|---|
load_alignments_msa.pl
| argument | default | description |
|---|---|---|
split_clustal.pl
| argument | default | description |
|---|---|---|
