EMBOSS: showdb

showdb

Function

Displays information on the currently available databases

Description

This writes out a simple table displaying the names, contents and available ways of accessing the sequence databases.

The available ways of accessing the databases are 'ID', 'Query' and 'All'. These refer to the way that you can search the databases to get entries from them, which is governed by the ways the database has been set up and the way it is organised and indexed.

Different databases may have different access capabilities, depending on how your local site is organised.

EMBOSS has been designed to be extremely flexible in its use of sequence databases formats, so that it is easy to set EMBOSS up to use your site's existing databases. Sometimes this means that it is hard to extract entries from some databases in particular ways. For example, a flat file database with no index is only useful for reading all entries, while a database located in another site that is available via the WWW may only provide single entries.

'ID' (also known as 'single entry') allows the programs to extract a single explicitly named entry from the database, for example embl:x13776

'Query' (also known as 'wild') indicates that programs can extract a set of matching wildcard entry names (this may be slow for some methods of access). For example you can look at all of the human PAX proteins in SWISS_PROT by: swissprot:pax*_human

'All' allows the programs to analyse all the entries in the database sequentially. For example this lets you look at all entries in the database with the notation: embl:*

A database may have several different methods of access available. Ideally all of the databases available on your site will be available in all three ways, but this is not the best of all posssible worlds and so you might like to check how you can access the databases by running this program and having a look.

Usage

Here is a sample session with showdb

Display information on the currently available databases:

% showdb Displays information on the currently available databases # Name Type ID Qry All Comment # ============== ==== == === === ======= qapblast P OK OK OK BLAST swissnew qapblastall P OK OK OK BLAST swissnew, all fields indexed qapblastsplit P OK OK OK BLAST swissnew split in 5 files qapblastsplitexc P OK OK OK BLAST swissnew split in 5 files, not file 02 qapblastsplitinc P OK OK OK BLAST swissnew split in 5 files, only file 02 qapfasta P OK OK OK FASTA file swissnew entries qapflat P OK OK OK SpTrEmbl flatfile qapflatall P OK OK OK SpTrEmbl flatfiles, all fields indexed qapir P OK OK OK PIR qapirall P OK OK OK PIR qapirinc P OK OK OK PIR qapxfasta P OK OK OK FASTA file swissnew entries qapxflat P OK OK OK Swissnew flatfiles qaxpir P OK OK OK PIR qaxpirall P OK OK OK PIR qaxpirinc P OK OK OK PIR tpir P OK OK OK PIR using NBRF access for 4 files tsw P OK OK OK Swissprot native format with EMBL CD-ROM index tswnew P OK OK OK SpTrEmbl as 3 files in native format with EMBL CD-ROM index twp P OK OK OK EMBL new in native format with EMBL CD-ROM index genbanksrs N OK - - Genbank IDs qanfasta N OK OK OK FASTA file EMBL rodents qanfastaall N OK OK OK FASTA file EMBL rodents, all fields indexed qanflat N OK OK OK EMBL flatfiles qanflatall N OK OK OK EMBL flatfiles qanflatexc N OK OK OK EMBL flatfiles, no rodent file qanflatinc N OK OK OK EMBL flatfiles, only rodent file qangcg N OK OK OK GCG format EMBL qangcgall N OK OK OK GCG format EMBL qangcgexc N OK OK OK GCG format EMBL without prokaryotes qangcginc N OK OK OK GCG format EMBL only prokaryotes qanxfasta N OK OK OK FASTA file EMBL rodents qanxfastaall N OK OK OK FASTA file EMBL rodents, all fields indexed qanxflat N OK OK OK EMBL flatfiles qanxflatall N OK OK OK EMBL flatfiles, all fields indexed qanxflatexc N OK OK OK EMBL flatfiles, no rodent file qanxflatinc N OK OK OK EMBL flatfiles, only rodent file qanxgcg N OK OK OK GCG format EMBL qanxgcgall N OK OK OK GCG format EMBL qanxgcgexc N OK OK OK GCG format EMBL without prokaryotes qanxgcginc N OK OK OK GCG format EMBL only prokaryotes qapirexc N OK OK OK PIR qasrswww N OK - - Remote SRS web server qawfasta N OK OK OK FASTA file wormpep entries qawxfasta N OK OK OK FASTA file wormpep entries qaxpirexc N OK OK OK PIR tembl N OK OK OK EMBL in native format with EMBL CD-ROM index temblall N - - OK EMBL in native format with EMBL CD-ROM index temblrest N - - OK EMBL in native format with EMBL CD-ROM index temblvrt N - - OK EMBL in native format with EMBL CD-ROM index testdb N OK OK OK test sequence data tgb N OK - - Genbank IDs tgenbank N OK OK OK GenBank in native format with EMBL CD-ROM index

Example 2

Write the results to a file:

% showdb -outfile showdb.out Displays information on the currently available databases

Go to the output files for this example

Example 3

Display information on one explicit database:

% showdb -database tsw Displays information on the currently available databases # Name Type ID Qry All Comment # ============ ==== == === === ======= tsw P OK OK OK Swissprot native format with EMBL CD-ROM index

Go to the input files for this example

Example 4

Display information on the databases formatted in HTML:

% showdb -html Displays information on the currently available databases

Name Type ID Qry All Comment

qapblast P OK OK OK BLAST swissnew

qapblastall P OK OK OK BLAST swissnew, all fields indexed

qapblastsplit P OK OK OK BLAST swissnew split in 5 files

qapblastsplitexc P OK OK OK BLAST swissnew split in 5 files, not file 02

qapblastsplitinc P OK OK OK BLAST swissnew split in 5 files, only file 02

qapfasta P OK OK OK FASTA file swissnew entries

qapflat P OK OK OK SpTrEmbl flatfile

qapflatall P OK OK OK SpTrEmbl flatfiles, all fields indexed

qapir P OK OK OK PIR

qapirall P OK OK OK PIR

qapirinc P OK OK OK PIR

qapxfasta P OK OK OK FASTA file swissnew entries

qapxflat P OK OK OK Swissnew flatfiles

qaxpir P OK OK OK PIR

qaxpirall P OK OK OK PIR

qaxpirinc P OK OK OK PIR

tpir P OK OK OK PIR using NBRF access for 4 files

tsw P OK OK OK Swissprot native format with EMBL CD-ROM index

tswnew P OK OK OK SpTrEmbl as 3 files in native format with EMBL CD-ROM index

twp P OK OK OK EMBL new in native format with EMBL CD-ROM index

genbanksrs N OK - - Genbank IDs

qanfasta N OK OK OK FASTA file EMBL rodents

qanfastaall N OK OK OK FASTA file EMBL rodents, all fields indexed

qanflat N OK OK OK EMBL flatfiles

qanflatall N OK OK OK EMBL flatfiles

qanflatexc N OK OK OK EMBL flatfiles, no rodent file

qanflatinc N OK OK OK EMBL flatfiles, only rodent file

qangcg N OK OK OK GCG format EMBL

qangcgall N OK OK OK GCG format EMBL

qangcgexc N OK OK OK GCG format EMBL without prokaryotes

qangcginc N OK OK OK GCG format EMBL only prokaryotes

qanxfasta N OK OK OK FASTA file EMBL rodents

qanxfastaall N OK OK OK FASTA file EMBL rodents, all fields indexed

qanxflat N OK OK OK EMBL flatfiles

qanxflatall N OK OK OK EMBL flatfiles, all fields indexed

qanxflatexc N OK OK OK EMBL flatfiles, no rodent file

qanxflatinc N OK OK OK EMBL flatfiles, only rodent file

qanxgcg N OK OK OK GCG format EMBL

qanxgcgall N OK OK OK GCG format EMBL

qanxgcgexc N OK OK OK GCG format EMBL without prokaryotes

qanxgcginc N OK OK OK GCG format EMBL only prokaryotes

qapirexc N OK OK OK PIR

qasrswww N OK - - Remote SRS web server

qawfasta N OK OK OK FASTA file wormpep entries

qawxfasta N OK OK OK FASTA file wormpep entries

qaxpirexc N OK OK OK PIR

tembl N OK OK OK EMBL in native format with EMBL CD-ROM index

temblall N - - OK EMBL in native format with EMBL CD-ROM index

temblrest N - - OK EMBL in native format with EMBL CD-ROM index

temblvrt N - - OK EMBL in native format with EMBL CD-ROM index

testdb N OK OK OK test sequence data

tgb N OK - - Genbank IDs

tgenbank N OK OK OK GenBank in native format with EMBL CD-ROM index

Example 5

Display protein databases only:

% showdb -nonucleic Displays information on the currently available databases # Name Type ID Qry All Comment # ============== ==== == === === ======= qapblast P OK OK OK BLAST swissnew qapblastall P OK OK OK BLAST swissnew, all fields indexed qapblastsplit P OK OK OK BLAST swissnew split in 5 files qapblastsplitexc P OK OK OK BLAST swissnew split in 5 files, not file 02 qapblastsplitinc P OK OK OK BLAST swissnew split in 5 files, only file 02 qapfasta P OK OK OK FASTA file swissnew entries qapflat P OK OK OK SpTrEmbl flatfile qapflatall P OK OK OK SpTrEmbl flatfiles, all fields indexed qapir P OK OK OK PIR qapirall P OK OK OK PIR qapirinc P OK OK OK PIR qapxfasta P OK OK OK FASTA file swissnew entries qapxflat P OK OK OK Swissnew flatfiles qaxpir P OK OK OK PIR qaxpirall P OK OK OK PIR qaxpirinc P OK OK OK PIR tpir P OK OK OK PIR using NBRF access for 4 files tsw P OK OK OK Swissprot native format with EMBL CD-ROM index tswnew P OK OK OK SpTrEmbl as 3 files in native format with EMBL CD-ROM index twp P OK OK OK EMBL new in native format with EMBL CD-ROM index

Example 6

Display the information with no headings:

% showdb -noheading Displays information on the currently available databases qapblast P OK OK OK BLAST swissnew qapblastall P OK OK OK BLAST swissnew, all fields indexed qapblastsplit P OK OK OK BLAST swissnew split in 5 files qapblastsplitexc P OK OK OK BLAST swissnew split in 5 files, not file 02 qapblastsplitinc P OK OK OK BLAST swissnew split in 5 files, only file 02 qapfasta P OK OK OK FASTA file swissnew entries qapflat P OK OK OK SpTrEmbl flatfile qapflatall P OK OK OK SpTrEmbl flatfiles, all fields indexed qapir P OK OK OK PIR qapirall P OK OK OK PIR qapirinc P OK OK OK PIR qapxfasta P OK OK OK FASTA file swissnew entries qapxflat P OK OK OK Swissnew flatfiles qaxpir P OK OK OK PIR qaxpirall P OK OK OK PIR qaxpirinc P OK OK OK PIR tpir P OK OK OK PIR using NBRF access for 4 files tsw P OK OK OK Swissprot native format with EMBL CD-ROM index tswnew P OK OK OK SpTrEmbl as 3 files in native format with EMBL CD-ROM index twp P OK OK OK EMBL new in native format with EMBL CD-ROM index genbanksrs N OK - - Genbank IDs qanfasta N OK OK OK FASTA file EMBL rodents qanfastaall N OK OK OK FASTA file EMBL rodents, all fields indexed qanflat N OK OK OK EMBL flatfiles qanflatall N OK OK OK EMBL flatfiles qanflatexc N OK OK OK EMBL flatfiles, no rodent file qanflatinc N OK OK OK EMBL flatfiles, only rodent file qangcg N OK OK OK GCG format EMBL qangcgall N OK OK OK GCG format EMBL qangcgexc N OK OK OK GCG format EMBL without prokaryotes qangcginc N OK OK OK GCG format EMBL only prokaryotes qanxfasta N OK OK OK FASTA file EMBL rodents qanxfastaall N OK OK OK FASTA file EMBL rodents, all fields indexed qanxflat N OK OK OK EMBL flatfiles qanxflatall N OK OK OK EMBL flatfiles, all fields indexed qanxflatexc N OK OK OK EMBL flatfiles, no rodent file qanxflatinc N OK OK OK EMBL flatfiles, only rodent file qanxgcg N OK OK OK GCG format EMBL qanxgcgall N OK OK OK GCG format EMBL qanxgcgexc N OK OK OK GCG format EMBL without prokaryotes qanxgcginc N OK OK OK GCG format EMBL only prokaryotes qapirexc N OK OK OK PIR qasrswww N OK - - Remote SRS web server qawfasta N OK OK OK FASTA file wormpep entries qawxfasta N OK OK OK FASTA file wormpep entries qaxpirexc N OK OK OK PIR tembl N OK OK OK EMBL in native format with EMBL CD-ROM index temblall N - - OK EMBL in native format with EMBL CD-ROM index temblrest N - - OK EMBL in native format with EMBL CD-ROM index temblvrt N - - OK EMBL in native format with EMBL CD-ROM index testdb N OK OK OK test sequence data tgb N OK - - Genbank IDs tgenbank N OK OK OK GenBank in native format with EMBL CD-ROM index

Example 7

Display just a list of the available database names:

% showdb -noheading -notype -noid -noquery -noall -nocomment -auto qapblast qapblastall qapblastsplit qapblastsplitexc qapblastsplitinc qapfasta qapflat qapflatall qapir qapirall qapirinc qapxfasta qapxflat qaxpir qaxpirall qaxpirinc tpir tsw tswnew twp genbanksrs qanfasta qanfastaall qanflat qanflatall qanflatexc qanflatinc qangcg qangcgall qangcgexc qangcginc qanxfasta qanxfastaall qanxflat qanxflatall qanxflatexc qanxflatinc qanxgcg qanxgcgall qanxgcgexc qanxgcginc qapirexc qasrswww qawfasta qawxfasta qaxpirexc tembl temblall temblrest temblvrt testdb tgb tgenbank

Example 8

Display only the names and types:

% showdb -only -type Displays information on the currently available databases qapblast P qapblastall P qapblastsplit P qapblastsplitexc P qapblastsplitinc P qapfasta P qapflat P qapflatall P qapir P qapirall P qapirinc P qapxfasta P qapxflat P qaxpir P qaxpirall P qaxpirinc P tpir P tsw P tswnew P twp P genbanksrs N qanfasta N qanfastaall N qanflat N qanflatall N qanflatexc N qanflatinc N qangcg N qangcgall N qangcgexc N qangcginc N qanxfasta N qanxfastaall N qanxflat N qanxflatall N qanxflatexc N qanxflatinc N qanxgcg N qanxgcgall N qanxgcgexc N qanxgcginc N qapirexc N qasrswww N qawfasta N qawxfasta N qaxpirexc N tembl N temblall N temblrest N temblvrt N testdb N tgb N tgenbank N

Example 9

Display everything

% showdb -full Displays information on the currently available databases # Name Type ID Qry All Method Fields Defined Release Comment # ============== ==== == === === ========= ================= ======= ======= ======= qapblast P OK OK OK blast - special BLAST swissnew qapblastall P OK OK OK blast sv,des special BLAST swissnew, all fields indexed qapblastsplit P OK OK OK blast - special BLAST swissnew split in 5 files qapblastsplitexc P OK OK OK blast - special BLAST swissnew split in 5 files, not file 02 qapblastsplitinc P OK OK OK blast - special BLAST swissnew split in 5 files, only file 02 qapfasta P OK OK OK emblcd - special FASTA file swissnew entries qapflat P OK OK OK emblcd - special SpTrEmbl flatfile qapflatall P OK OK OK emblcd sv,des,org,key special SpTrEmbl flatfiles, all fields indexed qapir P OK OK OK gcg - special PIR qapirall P OK OK OK gcg des,org,key special PIR qapirinc P OK OK OK gcg - special PIR qapxfasta P OK OK OK emboss - special FASTA file swissnew entries qapxflat P OK OK OK emboss - special Swissnew flatfiles qaxpir P OK OK OK embossgcg - special PIR qaxpirall P OK OK OK embossgcg des,org,key special PIR qaxpirinc P OK OK OK embossgcg - special PIR tpir P OK OK OK gcg des,org,key special PIR using NBRF access for 4 files tsw P OK OK OK emblcd sv,des,org,key special 36 Swissprot native format with EMBL CD-ROM index tswnew P OK OK OK emblcd sv,des,org,key special 37 SpTrEmbl as 3 files in native format with EMBL CD-ROM index twp P OK OK OK emblcd des special 16 EMBL new in native format with EMBL CD-ROM index genbanksrs N OK - - srswww gi,sv,des,org,key global Genbank IDs qanfasta N OK OK OK emblcd - special FASTA file EMBL rodents qanfastaall N OK OK OK emblcd sv,des special FASTA file EMBL rodents, all fields indexed qanflat N OK OK OK emblcd - special EMBL flatfiles qanflatall N OK OK OK emblcd - special EMBL flatfiles qanflatexc N OK OK OK emblcd - special EMBL flatfiles, no rodent file qanflatinc N OK OK OK emblcd - special EMBL flatfiles, only rodent file qangcg N OK OK OK gcg - special GCG format EMBL qangcgall N OK OK OK gcg sv,des,org,key special GCG format EMBL qangcgexc N OK OK OK gcg - special GCG format EMBL without prokaryotes qangcginc N OK OK OK gcg - special GCG format EMBL only prokaryotes qanxfasta N OK OK OK emboss - special FASTA file EMBL rodents qanxfastaall N OK OK OK emboss sv,des special FASTA file EMBL rodents, all fields indexed qanxflat N OK OK OK emboss - special EMBL flatfiles qanxflatall N OK OK OK emboss des,org,key special EMBL flatfiles, all fields indexed qanxflatexc N OK OK OK emboss - special EMBL flatfiles, no rodent file qanxflatinc N OK OK OK emboss - special EMBL flatfiles, only rodent file qanxgcg N OK OK OK embossgcg - special GCG format EMBL qanxgcgall N OK OK OK embossgcg sv,des,org,key special GCG format EMBL qanxgcgexc N OK OK OK embossgcg - special GCG format EMBL without prokaryotes qanxgcginc N OK OK OK embossgcg - special GCG format EMBL only prokaryotes qapirexc N OK OK OK gcg - special PIR qasrswww N OK - - srswww sv,des,org,key special Remote SRS web server qawfasta N OK OK OK emblcd - special FASTA file wormpep entries qawxfasta N OK OK OK emboss - special FASTA file wormpep entries qaxpirexc N OK OK OK embossgcg - special PIR tembl N OK OK OK emblcd sv,des,org,key special 57 EMBL in native format with EMBL CD-ROM index temblall N - - OK direct sv,des,org,key special 57 EMBL in native format with EMBL CD-ROM index temblrest N - - OK direct sv,des,org,key special 57 EMBL in native format with EMBL CD-ROM index temblvrt N - - OK direct sv,des,org,key special 57 EMBL in native format with EMBL CD-ROM index testdb N OK OK OK emblcd des special 01 test sequence data tgb N OK - - srswww sv,des,org,key special Genbank IDs tgenbank N OK OK OK emblcd sv,des,org,key special 01 GenBank in native format with EMBL CD-ROM index

Command line arguments

   Standard (Mandatory) qualifiers: (none)
   Additional (Optional) qualifiers:
   -database           string     Name of a single database to give
                                  information on (Any string is accepted)
   -html               boolean    [N] Format output as an HTML table
   -[no]protein        boolean    [Y] Display protein databases
   -[no]nucleic        boolean    [Y] Display nucleic acid databases
   -full               boolean    [N] Display all columns
   -methods            boolean    [$(full)] This displays the access methods
                                  that can be used on this database, for all,
                                  query or ID access
   -fields             boolean    [$(full)] This displays the search fields
                                  that can be used on this database, other
                                  than the standard 'id' or 'acc' fields.
   -defined            boolean    [$(full)] This displays a short name for the
                                  file containing the database definition
   -release            boolean    [$(full)] Display 'release' column
   -outfile            outfile    [stdout] Output file name

   Advanced (Unprompted) qualifiers:
   -only               toggle     [N] This is a way of shortening the command
                                  line if you only want a few standard columns
                                  to be displayed. Instead of specifying:
                                  '-nohead -notype -noid -noquery -noall'
                                  to get only the comment output, you can
                                  specify
                                  '-only -comment'
   -heading            boolean    [@(!$(only))] Display column headings
   -type               boolean    [@(!$(only))] Display 'type' column
   -id                 boolean    [@(!$(only))] Display 'id' column
   -query              boolean    [@(!$(only))] Display 'qry' column
   -all                boolean    [@(!$(only))] Display 'all' column
   -comment            boolean    [@(!$(only))] Display 'comment' column

   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

Standard (Mandatory) qualifiers Allowed values Default

(none)

Additional (Optional) qualifiers Allowed values Default

-database Name of a single database to give information on Any string is accepted An empty string is accepted

-html Format output as an HTML table Boolean value Yes/No No

-[no]protein Display protein databases Boolean value Yes/No Yes

-[no]nucleic Display nucleic acid databases Boolean value Yes/No Yes

-full Display all columns Boolean value Yes/No No

-methods This displays the access methods that can be used on this database, for all, query or ID access Boolean value Yes/No $(full)

-fields This displays the search fields that can be used on this database, other than the standard 'id' or 'acc' fields. Boolean value Yes/No $(full)

-defined This displays a short name for the file containing the database definition Boolean value Yes/No $(full)

-release Display 'release' column Boolean value Yes/No $(full)

-outfile Output file name Output file stdout

Advanced (Unprompted) qualifiers Allowed values Default

-only This is a way of shortening the command line if you only want a few standard columns to be displayed. Instead of specifying: '-nohead -notype -noid -noquery -noall' to get only the comment output, you can specify '-only -comment' Toggle value Yes/No No

-heading Display column headings Boolean value Yes/No @(!$(only))

-type Display 'type' column Boolean value Yes/No @(!$(only))

-id Display 'id' column Boolean value Yes/No @(!$(only))

-query Display 'qry' column Boolean value Yes/No @(!$(only))

-all Display 'all' column Boolean value Yes/No @(!$(only))

-comment Display 'comment' column Boolean value Yes/No @(!$(only))

Standard (Mandatory) qualifiers	Allowed values	Default
(none)
Additional (Optional) qualifiers	Allowed values	Default
-database	Name of a single database to give information on	Any string is accepted	An empty string is accepted
-html	Format output as an HTML table	Boolean value Yes/No	No
-[no]protein	Display protein databases	Boolean value Yes/No	Yes
-[no]nucleic	Display nucleic acid databases	Boolean value Yes/No	Yes
-full	Display all columns	Boolean value Yes/No	No
-methods	This displays the access methods that can be used on this database, for all, query or ID access	Boolean value Yes/No	$(full)
-fields	This displays the search fields that can be used on this database, other than the standard 'id' or 'acc' fields.	Boolean value Yes/No	$(full)
-defined	This displays a short name for the file containing the database definition	Boolean value Yes/No	$(full)
-release	Display 'release' column	Boolean value Yes/No	$(full)
-outfile	Output file name	Output file	stdout
Advanced (Unprompted) qualifiers	Allowed values	Default
-only	This is a way of shortening the command line if you only want a few standard columns to be displayed. Instead of specifying: '-nohead -notype -noid -noquery -noall' to get only the comment output, you can specify '-only -comment'	Toggle value Yes/No	No
-heading	Display column headings	Boolean value Yes/No	@(!$(only))
-type	Display 'type' column	Boolean value Yes/No	@(!$(only))
-id	Display 'id' column	Boolean value Yes/No	@(!$(only))
-query	Display 'qry' column	Boolean value Yes/No	@(!$(only))
-all	Display 'all' column	Boolean value Yes/No	@(!$(only))
-comment	Display 'comment' column	Boolean value Yes/No	@(!$(only))

Input file format

None.

Input files for usage example 3

'tsw' is a sequence entry in the example protein database 'tsw'

Output file format

Output files for usage example 2

File: showdb.out

# Name           Type  ID  Qry All Comment
# ============== ==== ==  === === =======
qapblast         P    OK  OK  OK  BLAST swissnew
qapblastall      P    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit    P    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta         P    OK  OK  OK  FASTA file swissnew entries
qapflat          P    OK  OK  OK  SpTrEmbl flatfile
qapflatall       P    OK  OK  OK  SpTrEmbl flatfiles, all fields indexed
qapir            P    OK  OK  OK  PIR
qapirall         P    OK  OK  OK  PIR
qapirinc         P    OK  OK  OK  PIR
qapxfasta        P    OK  OK  OK  FASTA file swissnew entries
qapxflat         P    OK  OK  OK  Swissnew flatfiles
qaxpir           P    OK  OK  OK  PIR
qaxpirall        P    OK  OK  OK  PIR
qaxpirinc        P    OK  OK  OK  PIR
tpir             P    OK  OK  OK  PIR using NBRF access for 4 files
tsw              P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew           P    OK  OK  OK  SpTrEmbl as 3 files in native format with EMBL CD-ROM index
twp              P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM index
genbanksrs       N    OK  -   -   Genbank IDs
qanfasta         N    OK  OK  OK  FASTA file EMBL rodents
qanfastaall      N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanflat          N    OK  OK  OK  EMBL flatfiles
qanflatall       N    OK  OK  OK  EMBL flatfiles
qanflatexc       N    OK  OK  OK  EMBL flatfiles, no rodent file
qanflatinc       N    OK  OK  OK  EMBL flatfiles, only rodent file
qangcg           N    OK  OK  OK  GCG format EMBL
qangcgall        N    OK  OK  OK  GCG format EMBL
qangcgexc        N    OK  OK  OK  GCG format EMBL without prokaryotes
qangcginc        N    OK  OK  OK  GCG format EMBL only prokaryotes
qanxfasta        N    OK  OK  OK  FASTA file EMBL rodents
qanxfastaall     N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanxflat         N    OK  OK  OK  EMBL flatfiles
qanxflatall      N    OK  OK  OK  EMBL flatfiles, all fields indexed
qanxflatexc      N    OK  OK  OK  EMBL flatfiles, no rodent file
qanxflatinc      N    OK  OK  OK  EMBL flatfiles, only rodent file
qanxgcg          N    OK  OK  OK  GCG format EMBL
qanxgcgall       N    OK  OK  OK  GCG format EMBL
qanxgcgexc       N    OK  OK  OK  GCG format EMBL without prokaryotes
qanxgcginc       N    OK  OK  OK  GCG format EMBL only prokaryotes
qapirexc         N    OK  OK  OK  PIR
qasrswww         N    OK  -   -   Remote SRS web server
qawfasta         N    OK  OK  OK  FASTA file wormpep entries
qawxfasta        N    OK  OK  OK  FASTA file wormpep entries
qaxpirexc        N    OK  OK  OK  PIR
tembl            N    OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblall         N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblrest        N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblvrt         N    -   -   OK  EMBL in native format with EMBL CD-ROM index
testdb           N    OK  OK  OK  test sequence data
tgb              N    OK  -   -   Genbank IDs
tgenbank         N    OK  OK  OK  GenBank in native format with EMBL CD-ROM index

The output is a simple table.

Type 'P' indicates that this is a Protein database.

Type 'N' indicates that this is a Nucleic database.

'OK' under ID, Qry or All indicates that that access method can be used on this database. A '-' indicates that you cannot access this database in that way.

Note that 'OK' does not mean that the database is working correctly. It simply means that showdb has read the database definition correctly and that this method of access to the database should be possible.

If you are setting up a new database, then you should check that it works correctly by extracting entries from it using seqret.

When the -html qualifier is specified, then the output will be wrapped in HTML tags, ready for inclusion in a Web page. Note that tags such as <HTML>, <BODY>, </BODY> and </HTML> are not output by this program as the table of databases is expected to form only part of the contents of a web page - the rest of the web page must be supplied by the user.

Data files

The databases are specified in the files "emboss.defaults" for site wide definitions, and "~/.embossrc" for the user's own settings.

Notes

Note that 'OK' in the output does not mean that the database is working correctly. It simply means that showdb has read the database definition correctly and that this method of access to the database should be possible.

If you are setting up a new database, then you should check that it works correctly by extracting entries from it using seqret.

You can set up your own private databases by editing a file called '.embossrc' to contain database specifications.

You can set up public databases by editing the file '/usr/local/share/EMBOSS/emboss.default' (if you have the permission to do this).

The 'emboss.default' file will already have the definitions of the test databases in: tsw, tembl, tpir, etc. These are the databases that are used in the examples shown in the documentation of the programs.

For details of the database definitions, you should first read David's Administration Guide: http://emboss.sourceforge.net/docs/adminguide/ especially: http://emboss.sourceforge.net/docs/adminguide/adminguide/node4.html

See also: http://emboss.sourceforge.net/docs/themes/Databases.html for a lot of detail of the syntax of database definition.

Just because showdb can display the database definitions, it does NOT mean that the databases are set up correctly. You must now test them using seqret.

References

None.

Warnings

None.

Diagnostic Error Messages

"The database 'xyz' does not exist" You have supplied the name of a database with the -database qualifier, but that database does not exist as far as EMBOSS is concerned.

Exit status

It always exits with status 0, unless the above diagnostic message is displayed.

Known bugs

None noted.

Program name	Description
abiview	Reads ABI file and display the trace
cirdna	Draws circular maps of DNA constructs
infoalign	Information on a multiple sequence alignment
infoseq	Displays some simple information about sequences
lindna	Draws linear maps of DNA constructs
pepnet	Displays proteins as a helical net
pepwheel	Shows protein sequences as helices
prettyplot	Displays aligned sequences, with colouring and boxing
prettyseq	Output sequence with translated ranges
remap	Display sequence with restriction sites, translation etc
seealso	Finds programs sharing group names
showalign	Displays a multiple sequence alignment
showfeat	Show features of a sequence
showseq	Display a sequence with features, translation etc
sixpack	Display a DNA sequence with 6-frame translation and ORFs
textsearch	Search sequence documentation. Slow, use SRS and Entrez!
tfm	Displays a program's help documentation manual
whichdb	Search all databases for an entry
wossname	Finds programs by keywords in their one-line documentation

Author(s)

Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

Completed 6th August 1999.

Target users

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

Comments

None