e-mail submission of sequences
Richard E. Showalter
rich at vaxkiller.agi.org
Tue Jan 14 13:59:42 EST 1992
In article <61770 at netnews.upenn.edu> gustilo at pobox.upenn.edu writes:
> I was wondering if there is an e-mail address for the submission of sequences
> for the BLAST and fasta programs.
> any help would be appreciated
BLAST: blast at genbank.bio.net
FASTA: search at genbank.bio.net
Sequence Entry Retrieval: retrieve at genbank.bio.net
FASTA and RETRIEVAL: fileserv at gunbrf.bitnet
No one mentioned the fasta server at EMBL. There are advantages and
disadvantages to searching at these different server sites.
At Genbank you can search GENBANK, EMBL, SWISS-PROT and GENPEPT
databases. On the Internet the response is generally very fast. (sometimes
minutes) If a DNA sequence is used, only one strand is searched so the
reverse/complement must be submitted also if you need both strands searched.
Using the retrieve address you can get any of the sequences from the searched
databases mailed to you.
The Blast server at Genbank will let you search GENBANK, SWISS-PROT,
and PIR. It is also very fast. (sometimes minutes) You cannot retrieve PIR
sequences from Genbank's retrieve system.(In any way that I know of.)
At EMBL you can search GENBANK, EMBL, SWISS-PROT, and PIR databases.
If a DNA sequence is used both strands are searched automatically. You cannot
retrieve sequences from the PIR database from EMBL, but you can get any of the
other sequences you might want. This service is generally much slower for us
here in San Diego. (sometimes days)
At NBRF you can search the PIR database with a protein sequence or have
your DNA sequence translated into all six open reading frames and searched
against PIR. This service is also generally very slow for us. You can
retrieve PIR sequences from NBRF using the fileserver.
There are several places where you can get VAX/VMS .com or UNIX csh
shell scripts that will automate the process of formatting a mail search to be
submitted to any of the above mentioned sites. I have used some of the posted
material to create my own scripts that will take any sequence format and use
Don Gilberts READSEQ program to convert the sequence to the correct format, and
using Thon de Boer's CID program to determine if the sequence is DNA or
PROTEIN, ask you all the necessary questions about KTUP, number of alignment
etc. and mail the search off. I have also automated the retrieval using shell
scripts. I am not a programmer, so these may not look pretty, but they do the
job and avoid a lot of errors from inexperienced computer using scientists with
whom I have to deal with.(Including myself) Hope this helps.
The opinions expressed are my own and my only be true for our site. I am not
affiliated with any of the above mentioned services or sites. I am just a
happy user of their systems.
Rich Showalter: Research Scientist by trade, SysAdmin by necessity.
"Hey, hey, hey, hey, it was the DNA, hey, hey, hey, hey, that made me
this way." (Queen: News of the World) Internet: rich at vaxkiller.agi.org
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