Difference between revisions of "GBrowse syn Scripts"
From GMOD
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Example: | Example: | ||
| − | + | perl aln2hit -f clustalw my_alignments.aln >my_alignments.txt | |
| − | + | ||
* It accepts as input an alignment data file in formats recognized by BioPerl. For best results, use FASTA or CLUSTALW formats. | * It accepts as input an alignment data file in formats recognized by BioPerl. For best results, use FASTA or CLUSTALW formats. | ||
| + | * The -f option is the only command-line argument. It specifies the alignment file format | ||
* Take care to format the sequence IDs as described [http://gmod.org/wiki/GBrowse_syn_Database#Note_on_the_sequence_ID_syntax here]. | * Take care to format the sequence IDs as described [http://gmod.org/wiki/GBrowse_syn_Database#Note_on_the_sequence_ID_syntax here]. | ||
Revision as of 12:05, 5 December 2009
Contents
aln2hit.pl
aln2hit.pl is a generic alignment data parser that will generate a tab-delimited file suitable for loading into the GBrowse_syn alignment database.
Example:
perl aln2hit -f clustalw my_alignments.aln >my_alignments.txt
- It accepts as input an alignment data file in formats recognized by BioPerl. For best results, use FASTA or CLUSTALW formats.
- The -f option is the only command-line argument. It specifies the alignment file format
- Take care to format the sequence IDs as described here.
