EMBOSS: whichdb

| ## EMBOSS: whichdb

# Program 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
    Search all databases for an entry
    ID or Accession number: hsfau
    Output file [outfile.whichdb]:

## Command line arguments

       Mandatory qualifiers (* if not always prompted):
      [-entry]             string     ID or Accession number
    *  -outfile            outfile    Output file name

       Optional qualifiers: (none)
       Advanced qualifiers:
       -get                bool       Retrieve sequences

       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-entry] (Parameter 1) | ID or Accession number | Any string is accepted | An empty string is accepted
-outfile | Output file name | Output file | <sequence>.whichdb
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-get | Retrieve sequences | Yes/No | No

## Input file format

None.

## Output file format

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

The results from the above example follow:

    embl:hsfau
    human:hsfau
    tembl:hsfau
    em:hsfau
    genbank:hsfau
    gb:hsfau

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 text. SRS and Entrez are faster!
tfm | Displays a program's help documentation manual
wossname | Finds programs by keywords in their one-line documentation

## Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.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