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* MINORE: AUTOMATED SEARCH OF BIOLOGICAL SEQUENCE DATABASES *
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Giovanni Lavorgna (1), Barbara Mapelli (1), Maura Strigini (1) and
Edoardo Boncinelli (1,2).
(1) DIBIT, Istituto Scientifico H. S. Raffaele, Via Olgettina 60,
20132Milano;
(2) Centro Farmacologia Cellulare e Molecolare, CNR, Via Vanvitelli 32,
20129 Milano.
MINORE is now available by anonymous ftp in the directory /pub/unix/minore
at ftp.hsr.it.
MINORE is a new software tool for performing automated searches of
biological sequence databases. Program is based on a couple of UNIX
shell scripts, which perform periodic database searches
with one or more query sequences, parse the relative output file(s) and
alert the user (by sending him/her an E-mail message) if anything
interesting comes out from the search.
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The ever growing (very often on a daily basis) accumulation of
biological information in sequence databases grants the periodic effort
of screening such databases with query sequences of known or unknown
function, looking for statistically interesting new hits. However
this task becomes tedious and time consuming, especially when dealing
with several query sequences. Our program, MINORE, performs this task
routinely and in a completely automated way.
MINORE uses the BLAST E-mail server to search the biological
sequence databases at the National Centre for Biological Information
(NCBI). To this purpose, it sends a properly formatted sequence to this
server; then it parses the answer message, looking for matches with 'p'
values lower than a threshold value. If any are found, it keeps note
of this match and alerts the user by sending back an E-mail message. The
user is never alerted more than once for a match to the same sequence.
Since MINORE is an UNIX program, it can be run periodically and
without any intervention from the user by simply putting it the system
'crontab'.
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If you've problems, bug report or any proposal on how to improve MINORE
program, please contact me at the following address:
Giovanni Lavorgna
DIBIT-HSR
Via Olgettina, 58
20132 Milan ITALY
Tel. ++39-2-26434776
Fax ++39-2-26434767
E-mail lavorgg at dibit.hsr.it
