Flat DNA/Protein Sequence Retrieval Service by "whois"
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DNA and Protein sequences can be obtained by using "whois" command
in a local UNIX system on your desk.
It is possible to do keyword search in DNA/protein databases but
it often generates too much output so that sequence retrieval
by specifying entry names or accession numbers can be only allowed.
For fasta homology search and keyword search/retrieval,
use a "Flat DB E-Mail Network Server" which is also available
at smlab.eg.gunma-u.ac.jp. For a brief manual, send an empty mail
to flat-netserv at smlab.eg.gunma-u.ac.jp.
12/10/02
Sanzo Miyazawa
Gunma Univ., Faculty of Technology
FAX: +81 277 40 1026
Phone: +81 277 40 1027
E-mail: sanzo.miyazawa at smlab.eg.gunma-u.ac.jp
NAME
scandb - scan a database to find entries by entry name or
accession number
SYNOPSIS
% alias scandb "whois -h smlab.eg.gunma-u.ac.jp"
% scandb help
% scandb "_d_b-_n_a_m_e [ -1 ] [ -o ] [ '_e_n_t_r_y'...] [ | -a '#_a_c_c'... ]"
DESCRIPTION
Scandb scans the _d_b-_n_a_m_e database to find _e_n_t_r_i_e_s... or
#_a_c_c... . '_E_n_t_r_y' and '#_a_c_c' (acession numbers) are
expressed in the regular expression but the case of letters
is ignored. The following databases are available.
_d_b-_n_a_m_e = genbank | embl | genpept | swiss | pir | prf
genbank | gb
GenBank DNA database including regular release and
new entries
embl EMBL DNA database including regular release and
new entries.
genpept | gp
GenBank Gene Product Database
swiss
SwissProt protein database
pir PIR protein database
prf Peptide Research Foundation peptide database
"gb" and "embl" include new entries released by e-mail or
obtained by anonymous-FTP in addition to entries in their
regular release.
OPTIONS
-1 All entries with the specified name or accession number
in database are retrieved; otherwise only one entries
first found is retrieved; the first found entry is usu-
ally the most recently released one. To retrieve mul-
tiple entries by using wild characters, "-1" must be
specified. However, if a secondary accession number is
specified, multiple entries with the accession number
might be retrieved, even if "-1" is not used. If -o"
is specified, -1 will be assumed.
-o Entries are not retrieved in the specified order but in
the original order. Retrieval becomes faster.
-a must be specified if you want to retrieve entries by
accession number.
EXAMPLES
flat% scandb "genbank AGMERLTR1 musbas" # by entry name;case insensitive
flat% scandb "genbank -a M11391 d00611" # by accession number
ALSO
For fasta homology search and keyword search/retrieval,
use a "Flat DB E-Mail Network Server" which is also available
at smlab.eg.gunma-u.ac.jp. For a brief manual, send an empty mail
to flat-netserv at smlab.eg.gunma-u.ac.jp.
AUTHORS
Sanzo Miyazawa (smiyazaw at smlab.eg.gunma-u.ac.jp)
Gunma University, Faculty of Technology
1-5-1 Tenjin
Kiryu, Gunma 376
Japan
BUGS
This command somewhat takes time because of setting up an environment.
