I have an accession number, can I extract genbank information from an on-line database?

Thomas Siegmund siegmund at develogen.com
Wed Mar 12 11:28:25 UTC 2003

Hi Burke,

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 [
 methodentry: app
 app: "fastacmd  -d/data/blast/data/nt -s%s"
 type: N
 format: fasta
 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?
> Thanks!
> Burke Squires

Thomas Siegmund, Ph.D.
DeveloGen AG
Bioinformatics and Data Management
Phone: +49(551) 505 58 651

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