Bioperl: NCBI 'Query' email server

[Joe Ryan]

> exploration of these ideas, I came across the NCBI query email server
> which I am thinking will be a pretty decent way to grab sequences off
> NCBI in the absence of a more direct route. (is there a more direct
> route short of mirroring the database locally?)
> http://www.ncbi.nlm.nih.gov/Web/Search/email.html

Simon,

I would recommend using LWP and getting the sequences from Entrez.
Here is a simple command line that will fetch a protein sequence in
FASTA format with GI number = 2654005

perl -MLWP::Simple -e 'getprint "http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=6&db=p&dopt=f&dispmax=1&uidstring=2654005&save=UNIX&savehow=Text"'

Here is one that fetches a nucleotide sequence in FASTA format with 
Accession number = AI606610

perl -MLWP::Simple -e 'getprint "http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=6&db=n&dopt=f&dispmax=1&uidstring=AI606610&save=UNIX&savehow=Text"'

These require LWP which you can get from http://www.perl.com/CPAN/modules/by-module/WWW/libwww-perl-X.XX.tar.gz 

Good Luck,

Joe
--
Joseph Ryan
Programmer
National Human Genome Research Institute


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