> 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
