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.  


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:


(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





These are the sequences from Fred Blattner's group.



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

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