EMBOSS: whichdb manual

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: hsfau1
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
*  -outfile            outfile    Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -get                toggle     Retrieve sequences
   -showall            boolean    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 deaths

Standard (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
Additional (Optional) qualifiers		Allowed values	Default
(none)
Advanced (Unprompted) qualifiers		Allowed values	Default
-get	Retrieve sequences	Toggle value Yes/No	No
-showall	Show failed attempts	Boolean value Yes/No	No

Input file format

None.

Output file format

Output files for usage example

File: outfile.whichdb

# Trying 'qangcgall:hsfau1'
# Failed 'qangcgall:hsfau1'
# Trying 'twp:hsfau1'
# Failed 'twp:hsfau1'
# Trying 'qapblast:hsfau1'
# Failed 'qapblast:hsfau1'
# Trying 'tsw:hsfau1'
# Failed 'tsw:hsfau1'
# Trying 'qapblastsplit:hsfau1'
# Failed 'qapblastsplit:hsfau1'
# Trying 'qangcginc:hsfau1'
# Failed 'qangcginc:hsfau1'
# Trying 'qangcgexc:hsfau1'
# Failed 'qangcgexc:hsfau1'
# Trying 'qasrsfasta:hsfau1'
qasrsfasta:hsfau1
# Trying 'qapir:hsfau1'
# Failed 'qapir:hsfau1'
# Trying 'tgenbank:hsfau1'
tgenbank:hsfau1
# Trying 'qanfasta:hsfau1'
# Failed 'qanfasta:hsfau1'
# Trying 'qanxflat:hsfau1'
# Failed 'qanxflat:hsfau1'
# Trying 'qanxgcg:hsfau1'
# Failed 'qanxgcg:hsfau1'
# Trying 'qapflat:hsfau1'
# Failed 'qapflat:hsfau1'
# Trying 'qapblastsplitinc:hsfau1'
# Failed 'qapblastsplitinc:hsfau1'
# Trying 'qapblastsplitexc:hsfau1'
# Failed 'qapblastsplitexc:hsfau1'
# Trying 'qapflatall:hsfau1'
# Failed 'qapflatall:hsfau1'
# Trying 'qanxflatall:hsfau1'
qanxflatall:hsfau1
# Trying 'qapflatinc:hsfau1'
# Failed 'qapflatinc:hsfau1'
# Trying 'qapflatexc:hsfau1'
# Failed 'qapflatexc:hsfau1'
# Trying 'qasrs:hsfau1'
qasrs:hsfau1
# Trying 'qapxflatinc:hsfau1'
# Failed 'qapxflatinc:hsfau1'
# Trying 'qapxflatexc:hsfau1'
# Failed 'qapxflatexc:hsfau1'
# Trying 'tpir:hsfau1'
# Failed 'tpir:hsfau1'
# Trying 'qasrswww:hsfau1'
qasrswww:hsfau1
# Trying 'qanxfasta:hsfau1'
# Failed 'qanxfasta:hsfau1'
# Trying 'qanxgcgall:hsfau1'
# Failed 'qanxgcgall:hsfau1'
# Trying 'qangcg:hsfau1'
# Failed 'qangcg:hsfau1'
# Trying 'qanfastaall:hsfau1'
# Failed 'qanfastaall:hsfau1'
# Trying 'qapirall:hsfau1'
# Failed 'qapirall:hsfau1'
# Trying 'qanxgcginc:hsfau1'
# Failed 'qanxgcginc:hsfau1'
# Trying 'qanxgcgexc:hsfau1'
# Failed 'qanxgcgexc:hsfau1'
# Trying 'qapirinc:hsfau1'
# Failed 'qapirinc:hsfau1'
# Trying 'qanflat:hsfau1'
# Failed 'qanflat:hsfau1'
# Trying 'qanxfastaall:hsfau1'
# Failed 'qanxfastaall:hsfau1'
# Trying 'qapfasta:hsfau1'
# Failed 'qapfasta:hsfau1'
# Trying 'qawxfasta:hsfau1'
# Failed 'qawxfasta:hsfau1'
# Trying 'qapirexc:hsfau1'
# Failed 'qapirexc:hsfau1'
# Trying 'tswnew:hsfau1'
# Failed 'tswnew:hsfau1'
# Trying 'qaxpirall:hsfau1'
# Failed 'qaxpirall:hsfau1'
# Trying 'qapxflat:hsfau1'
# Failed 'qapxflat:hsfau1'
# Trying 'qaxpirinc:hsfau1'
# Failed 'qaxpirinc:hsfau1'
# Trying 'qapxfasta:hsfau1'
# Failed 'qapxfasta:hsfau1'
# Trying 'tembl:hsfau1'
tembl:hsfau1
# Trying 'qaxpirexc:hsfau1'
# Failed 'qaxpirexc:hsfau1'
# Trying 'qapblastall:hsfau1'
# Failed 'qapblastall:hsfau1'
# Trying 'tgb:hsfau1'
# Failed 'tgb:hsfau1'
# Trying 'qaxpir:hsfau1'
# Failed 'qaxpir:hsfau1'
# Trying 'qawfasta:hsfau1'
# Failed 'qawfasta:hsfau1'

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.

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

Function

Description

IDs and Accessions

Usage

Command line arguments

Input file format

Output file format

Output files for usage example

File: outfile.whichdb

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments