Difference between revisions of "GBrowse syn Scripts"
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| − | |Specifies the alignment file format. MOst common formats recongnized by BioPerl's [http://doc.bioperl.org/releases/bioperl-1.0/Bio/AlignIO.html AlignIO parsers] are supported | + | |Specifies the alignment file format. MOst common formats recongnized by BioPerl's [http://doc.bioperl.org/releases/bioperl-1.0/Bio/AlignIO.html AlignIO parsers] are supported. Use [http://www.bioperl.org/wiki/ClustalW_multiple_alignment_format clustalw] or [http://www.bioperl.org/wiki/FASTA_multiple_alignment_format fasta] for best results. |
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!i | !i | ||
Revision as of 12:21, 5 December 2009
Contents
aln2hit.pl
aln2hit.pl is a generic alignment data parser that comverts alignment data into the GBrowse_syn database loading format.
You would use this script in cases where you have a single alignment file (in a supported format) and want to convert it to the tab-delimited format that is used to load the 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 |
- Take care to format the sequence IDs as described here.
clustal2hit.pl
| argument | default | description |
|---|---|---|
load_alignment_database.pl
| argument | default | description |
|---|---|---|
load_alignments_gff3.pl
| argument | default | description |
|---|---|---|
load_alignments_msa.pl
| argument | default | description |
|---|---|---|
mercatoraln_to_synhits.pl
| argument | default | description |
|---|---|---|
split_clustal.pl
| argument | default | description |
|---|---|---|
