
                                  whichdb 



Function

   Search all databases for an entry

Description

   whichdb searches all available EMBOSS databases for sequences with a
   specified ID name or accession number.

   EMBOSS does not allow database entries to be specified by just the ID
   name or accession number. You must specify both the name of the
   database and the entry, for example 'embl:hsfau', not just 'hsfau'.

   If you do not know which database(s) contain the entry you are
   interested in, whichdb will tell you.

   whichdb can also, optionally, write out the sequences it finds to
   files.

  IDs and Accessions

   An entry in a database must have some way of being uniquely identified
   in that database. Most sequence databases have two such identifiers
   for each sequence - an ID name and an Accession number.

   Why are there two such identifiers? The ID name was originally
   intended to be a human-readable name that had some indication of the
   function of its sequence. In EMBL and GenBank the first two (or three)
   letters indicated the species and the rest indicated the function, for
   example 'hsfau' is the 'Homo Sapiens FAU pseudogene'. This naming
   scheme started to be a problem when the number of entries added each
   day was so vast that people could not make up the ID names fast
   enough. Instead, the Accession numbers were used as the ID name.
   Therefore you will now find ID names like 'AF061303', the same as the
   Accession number for that sequence in EMBL.

   ID names are not guaranteed to remain the same between different
   versions of a database (although in practice they usually do).

   Accession numbers are unique alphanumeric identifiers that are
   guaranteed to remain with that sequence through the rest of the life
   of the database. If two sequences are merged into one, then the new
   sequence will get a new Accession number and the Accession numbers of
   the merged sequences will be retained as 'secondary' Accession
   numbers.

   EMBL, GenBank and SwissProt share an Accession numbering scheme - an
   Accession number uniquely identifies a sequence within these three
   databases.

Usage

   Here is a sample session with whichdb


% whichdb -showall 
Search all databases for an entry
ID or Accession number: x65921
Output file [outfile.whichdb]: 

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-entry]             string     ID or Accession number (Any string is
                                  accepted)
*  -outfile            outfile    [*.whichdb] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -get                toggle     [N] Retrieve sequences
   -showall            boolean    [N] Show failed attempts

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

   None.

Output file format

  Output files for usage example

  File: outfile.whichdb

# Trying 'qanflatall:x65921'
qanflatall:x65921
# Trying 'qangcgall:x65921'
# Failed 'qangcgall:x65921'
# Trying 'twp:x65921'
# Failed 'twp:x65921'
# Trying 'qapblast:x65921'
# Failed 'qapblast:x65921'
# Trying 'tsw:x65921'
# Failed 'tsw:x65921'
# Trying 'qanflatinc:x65921'
# Failed 'qanflatinc:x65921'
# Trying 'qapblastsplit:x65921'
# Failed 'qapblastsplit:x65921'
# Trying 'qangcginc:x65921'
# Failed 'qangcginc:x65921'
# Trying 'qanflatexc:x65921'
qanflatexc:x65921
# Trying 'qangcgexc:x65921'
# Failed 'qangcgexc:x65921'
# Trying 'qapir:x65921'
# Failed 'qapir:x65921'
# Trying 'tgenbank:x65921'
tgenbank:x65921
# Trying 'qanfasta:x65921'
# Failed 'qanfasta:x65921'
# Trying 'qanxflat:x65921'
# Failed 'qanxflat:x65921'
# Trying 'qanxgcg:x65921'
# Failed 'qanxgcg:x65921'
# Trying 'qapflat:x65921'
# Failed 'qapflat:x65921'
# Trying 'qapblastsplitinc:x65921'
# Failed 'qapblastsplitinc:x65921'
# Trying 'qapblastsplitexc:x65921'
# Failed 'qapblastsplitexc:x65921'
# Trying 'qapflatall:x65921'
# Failed 'qapflatall:x65921'
# Trying 'qanxflatall:x65921'
qanxflatall:x65921
# Trying 'qanxflatinc:x65921'
# Failed 'qanxflatinc:x65921'
# Trying 'qanxflatexc:x65921'
qanxflatexc:x65921
# Trying 'testdb:x65921'
# Failed 'testdb:x65921'
# Trying 'genbanksrs:x65921'
genbanksrs:x65921
# Trying 'tpir:x65921'
# Failed 'tpir:x65921'
# Trying 'qasrswww:x65921'
qasrswww:x65921
# Trying 'qanxfasta:x65921'
# Failed 'qanxfasta:x65921'
# Trying 'qanxgcgall:x65921'
# Failed 'qanxgcgall:x65921'
# Trying 'qangcg:x65921'
# Failed 'qangcg:x65921'
# Trying 'qanfastaall:x65921'
# Failed 'qanfastaall:x65921'
# Trying 'qapirall:x65921'
# Failed 'qapirall:x65921'
# Trying 'qanxgcginc:x65921'
# Failed 'qanxgcginc:x65921'
# Trying 'qanxgcgexc:x65921'
# Failed 'qanxgcgexc:x65921'
# Trying 'qapirinc:x65921'
# Failed 'qapirinc:x65921'
# Trying 'qanflat:x65921'
# Failed 'qanflat:x65921'
# Trying 'qanxfastaall:x65921'
# Failed 'qanxfastaall:x65921'
# Trying 'qapfasta:x65921'
# Failed 'qapfasta:x65921'
# Trying 'qawxfasta:x65921'
# Failed 'qawxfasta:x65921'
# Trying 'qapirexc:x65921'
# Failed 'qapirexc:x65921'
# Trying 'tswnew:x65921'
# Failed 'tswnew:x65921'
# Trying 'qaxpirall:x65921'
# Failed 'qaxpirall:x65921'
# Trying 'qapxflat:x65921'
# Failed 'qapxflat:x65921'
# Trying 'qaxpirinc:x65921'
# Failed 'qaxpirinc:x65921'
# Trying 'qapxfasta:x65921'
# Failed 'qapxfasta:x65921'
# Trying 'tembl:x65921'
tembl:x65921
# Trying 'qaxpirexc:x65921'
# Failed 'qaxpirexc:x65921'
# Trying 'qapblastall:x65921'
# Failed 'qapblastall:x65921'
# Trying 'tgb:x65921'
tgb:x65921
# Trying 'qaxpir:x65921'
# Failed 'qaxpir:x65921'
# Trying 'qawfasta:x65921'
# Failed 'qawfasta:x65921'

   The reported database entries are written out to the specified output
   file.

   Each database that is defined in the local implementation of EMBOSS
   which contains an entry called 'hsfau' is reported.

   Note that where a database is defined under several names ('embl',
   'em'), each definition of that database containing the entry is
   reported.

   When the '-get' option is used to output the sequences, they are
   written to separate files. The sequence format they are written in is
   always 'Fasta' format. The normal command-line qualifiers for changing
   the output formats etc. will not work in this program.

   The names of the files that the sequences are written to is reported
   as they are written, for example:

Writing hsfau.embl
Writing hsfau.human
Writing hsfau.tembl
Writing hsfau.em
Writing hsfau.genbank
Writing hsfau.gb

Data files

   None.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name                        Description
   infoalign    Information on a multiple sequence alignment
   infoseq      Displays some simple information about sequences
   seealso      Finds programs sharing group names
   showdb       Displays information on the currently available databases
   textsearch   Search sequence documentation. Slow, use SRS and Entrez!
   tfm          Displays a program's help documentation manual
   wossname     Finds programs by keywords in their one-line documentation

Author(s)

   Alan Bleasby (ajb © ebi.ac.uk)
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

History

   Written (Jan 2002) - Alan Bleasby.

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
