DNA/Protein sequence retrieval by "whois"

Sanzo Miyazawa smiyazaw at smss2.smlab.eg.gunma-u.ac.jp
Thu Dec 10 06:00:20 EST 1992


	Flat DNA/Protein Sequence Retrieval Service by "whois"
	------------------------------------------------------


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.




More information about the Bio-soft mailing list