smiyazaw@smlab.eg.gunma-u.ac.jp (Sanzo Miyazawa) (06/10/91)
FLAT DB E-Mail Network Server in Japan
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Sanzo Miyazawa
smiyazaw@smlab.eg.gunma-u.ac.jp
FLAT E-mail network server for DNA/protein databases is now available at
flat-netserv@smlab.eg.gunma-u.ac.jp in Japan, which is reachable via Internet,
Bitnet, Csnet, Janet, Junet, and others.
One of characteristics in this database server is that it provides a function
of keyword serach over database entries such as author name, Journal name,
and any sequence description.
Available databases are
GenBank; regular release + new entries retrieved from "Bionet".
EMBL; regular release + new entries
DDBJ
GenPept
SwissProt
PIR
PRF (Protein Research Foundation peptide database)
The following is a brief manual for this database server.
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FLAT DB E-Mail Network Server
Sanzo Miyazawa
smiyazaw@smlab.eg.gunma-u.ac.jp
Gunma Univ., Faculty of Technology
FAX: +81 277 40 1026
Phone: +81 277 22 3181 ext. 262
E-mail address for the server: flat-netserv@smlab.eg.gunma-u.ac.jp
or netserv@smlab.eg.gunma-u.ac.jp
E-mail address for inquiries: sanzo.miyazawa@smlab.eg.gunma-u.ac.jp
or smiyazaw@smlab.eg.gunma-u.ac.jp
Following commands are available:
- Commands must be written not at the "Subject:" field but in a mail.
- Command names and others are case sensitive, unless specified.
- Output may be limited to 2400 lines.
- Character strings may be represented in the regular expression.
scandir db-name [options] 'keyword[|keyword...]' ['keyword[|keyword...]'] ...
Scan directory files of the "db-name" database to find "keywords"
and output entry names and their definitions; keywords should be
expressed in the regular expression, that is,
key-1|key-2 key3 means "(key-1 or key-2) and key-3"
Options:
-i case insensitive
scanjou db-name ['journal'] ['vol:'['page[-page]']] ['(year)']
Scan journal index files of the "db-name" database to find specified
journals and output journal names and corresponding entry names.
Journal names in the command line are not case sensitive.
scanaut db-name 'Last-name,[First.Middle-Initial.]' ...
Scan author index files of the "db-name" database to find specified
author names and output author names and corresponding entry names
with their definitions.
Author names in the command line are not case sensitive.
scanacc db-name '#acc' ...
Scan accession number index files of the "db-name" database to find
specified accession numbers and output corresponding entry names
with their definitions.
scandb db-name [-1] [-o] {['entry'...]|[-a '#acc'...]}
Scan the "db-name" database to find specified entries or accession
numbers and output those entries.
Options:
-1 'Entry' or '#acc' may specify multiple entries in the DB.
-o The order of arguments is not significant; the order of entries
output may not be in the order specified in the command line.
Available databases:
db-name = gb | embl | ddbj | gp | swiss | pir | prf
gb or genbank: GenBank DNA database
Regular release and new entries which are updated
twice a day.
embl: EMBL DNA database; regular release + new entries
ddbj: DDBJ DNA database; regular release + new entries
It is included in the GenBank and EMBL DBs.
gp or genpept: GenBank Gene Product Database;
protein database translated from GenBank DNA database
swiss: SwissProt protein database
pir: PIR protein database
prf: Protein Research Foundation peptide database
Examples:
"|" is not ";" but "bar".
scandir gb -i 'oncogene' 'human' # oncogene and human
scanjou gb 'J. Biochem.' '107:316-323' '(1990)' # case insensitive
scanaut gb 'Miyazawa,S.' # case insensitive
scanacc gb 'M11391' 'd00611' # case insensitive
scandb gb 'AGMERLTR1' 'musbas' # case insensitive
scandb gb -a 'M11391' 'd00611' # case insensitive
scandb gb 'ECO.*' # all ECO.*
scandir gb -i ' e.*coli' | scandb gb # try to collect E. coli
scanjou gb 'J. Biochem,' '(1991)' | scandb gb
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