[Gmod-gbrowse] [Gmod-help] intergenic sequences from gff file and genome

[Don Gilbert]

Here is a perl script I use for this kind of thing.  However it
comes without good documentation or support.  If you have some
perl and sequence skills, it may get you going. See here for
program and sample use:

  http://wfleabase.org/genome-summaries/gene-structure/basecounts/
  http://wfleabase.org/genome-summaries/gene-structure/basecounts/cdsgff2seq.pl

    # pull sequence 99 bases outside of gene start, end to 9 bases inside:
  perl cdsgff2seq.pl -a genestart -offset=-99,9 -type exon \
    -gff daphniagenes.gff -fasta daphniagenome.fa > dpx-genestarts.fa

  perl cdsgff2seq.pl -a geneend -offset=-9,99 -type exon \
    -gff daphniagenes.gff -fasta daphniagenome.fa > dpx-geneends.fa

Another option is overkill for your need, the GMOD Bulktools program
(part of http://gmod.org/GMODTools) will produce intergenic
sequences as one output option.  You need however a GMOD Chado
database with your data to start.


- Don Gilbert
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd at indiana.edu--http://marmot.bio.indiana.edu/