genbank ORFs > fasta ??

francis at NCBI.NLM.NIH.GOV francis at NCBI.NLM.NIH.GOV
Sun Jul 6 23:50:20 EST 1997


> From trevor at leland.stanford.edu Mon Jul  7 00:18:38 1997

> Is there any program out there that converts files in standard genbank
> nucleotide format into a fasta file with all of the ORF translations?  All
> of the information is in the file, it would just be a pain to do it by
> hand.  

Trevor,

there is readseq (from Don Gilbert), but I doubt it will work on the
E.coli genome! If you do a www search with "gilbert readseq" you will
get quite a few hits!  Here is one possibility:

ftp://iubio.bio.indiana.edu/molbio/readseq/

(but there are many other implementation on the www)

> Otherwise, is there any copies of the E.coli genome with the
> translated ORFs in fasta form?

yes, we maintain these at NCBI, as we have them as blastable databases.
for our various BLAST serveices

See:

ftp://ncbi.nlm.nih.gov/blast/db/ecoli.aa.Z

and:

ftp://ncbi.nlm.nih.gov/blast/db/ecoli.nt.Z

These are the sequences from Fred Blattner's group.

regards,

francis

--
| B.F. Francis Ouellette  
| GenBank Coordinator
|
| francis at ncbi.nlm.nih.gov   




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