[Bioperl-l] Newbie gbrowse help - script to make gff from fasta

Jim Hu jim.hu.biobio at gmail.com
Sat Jul 30 16:05:42 EDT 2005

1) Is there an existing script to convert a refseq fasta into a gff  
flatfile compatible with gbrowse 1.62?

        bp_genbank2gff.pl --accession NC_001416  --stdout > lambda.gff

requires some additional tweaking/parsing as far as I can tell.  I  
know that I'll probably eventually load these into mySQL (but for  
phage genomes, is it worth it?), but I wanted to learn via the  
flatfiles first.

2) Is there a repository of standard track stanzas and aggregators  
that match the feature types generated by such scripts?

3) Is there a FAQ I missed that I should have consulted first?

4) Is this even the right listserv for these questions?

Didn't want to reinvent any wheels if possible.  Sorry if this is off  
topic.  Thanks!

Jim Hu

More information about the Bioperl-l mailing list