auto-mail program for BLAST?
Thon de Boer
deboer at bio.vu.nl
Mon Oct 5 08:31:58 EST 1992
theiss at CSHL.ORG (Bobbie Peters in Grace) writes:
: We have a program here that sends parameters & sequences to the old
: FASTA e-mail address in the correct format. It would ask the user questions -
: What is the name of the sequence, what databank do you want to search against,
: are these parameters OK, etc. Then it mailed the info to the old
: fasta bio.net address.
: I seem to remember that someone else offered the same type of program
: ages ago for FASTA. Rather than us re-writing the fasta program,
: has anyone written an auto mail program for BLAST?
: Along the same lines, is there a list of programs like BLAST, SeqApp, etc
: that are available via e-mail? This doesn't seem to be a question that
: Archie would easily answer.
There are several of those programs available for different computers.
There is GenBankSearch at NCBI for the MAC by Don Gilbert
NCBI en GRAIL shells for VMS by Foteos Macrides and
mailfasta3.0 for UNIX platforms, which I wrote.
You can find most of these programs at the iubio ftp server (fly.bio.indiana.edu)
and mailfasta3.0 can also be retrieved directly from me by ftp to bio.vu.nl /molbio
and through a gopher hole at grampus.bio.vu.nl at port 9001.
Sincerely, Thon de Boer
Here is the announcement of mailfasta3.0
This is version 3.0 of the mailfasta program. It is a UNIX shell script which
will take a DNA or PROTEIN sequence and will mail it to all the
different mail-servers where it can be searched against the DNA or PROTEIN
databases using the FASTA and/or BLAST programs. It can also be used to identify
ORFs using the GRAIL and/or GeneID/NetGene mail servers and to identify homology
using PROSITE blocks with the BLOCKS server.
It uses the new BLAST server at NCBI and the FLAT server in Japan for FASTA
searches because the services at GenBank will be terminated at the end of this
It is packed as an shell archive. It contains :
mailfasta : the UNIX shell script
cid.c : A small c program which will determine if the sequence is DNA or AA
getentry : A shell script which can be used to retrieve entries of interest
mailfasta.doc : The documentation file
The shar file will unpack all these files and will compile cid.c into cid
using the cc c compiler.
mailfasta makes use oif the program 'readseq' for file conversion.
This program MUST be present and is NOT packed with this shar file.
It can be obtained via FTP from various FTP sites (fly.bio.indiana.edu etc.)
This shar file can also be found on this FTP site. First in the 'incomming'
directory and later in the /molbio/unix directory.
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