I have an accession number, can I extract genbank information from an on-line database?
siegmund at develogen.com
Wed Mar 12 11:28:25 UTC 2003
if you have blast databases in house, you can use fastacmd (comes with blast)
to extract single sequences in fasta format from the binary database.
With a emboss.default like this you can access the blast database in EMBOSS:
DB nt [
app: "fastacmd -d/data/blast/data/nt -s%s"
comment: "nt - non redundant nucleotide sequences"
Am Mittwoch, 12. März 2003 05:03 schrieb Burke Squires:
> Hello EMBOSSers,
> Is it possible to extract genbank file information from an on-line database
> if I have an accession number or do I have to download the hundreds of
> genbank files locally and extract it from that? If so how? I have read
> information on seqret and it seems truly wonderful but it seems to work
> only with local databases?
> Burke Squires
Thomas Siegmund, Ph.D.
Bioinformatics and Data Management
Phone: +49(551) 505 58 651
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