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

Scott Cain cain at cshl.edu
Mon Aug 1 14:13:12 EDT 2005

On Sat, 2005-07-30 at 15:05 -0500, Jim Hu wrote:
> 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.

I assume you mean genbank files, as there wouldn't be much to convert
from a fasta file.  Anyway, you should also try bp_genbank2gff3.pl.  Be
warned however, that converting genbank files to anything more stringent
like GFF3 is fiendishly difficult, and depending on the genbank file,
you may need to massage the output.
> 2) Is there a repository of standard track stanzas and aggregators  
> that match the feature types generated by such scripts?

In the distribution are several example configuration files in
> 3) Is there a FAQ I missed that I should have consulted first?

No, but there is a tutorial that comes with GBrowse that covers lots of
useful material.  You can find it at

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

Yes, and welcome!
> Didn't want to reinvent any wheels if possible.  Sorry if this is off  
> topic.  Thanks!
> Jim Hu
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Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

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