showdb |
showdb displays a table with the names, contents and access methods of the sequence databases configured for your EMBOSS installation.
Display information on the currently available databases:
% showdb Displays information on configured databases # Name Type ID Qry All Comment # ============== ==== == === === ======= twp P OK OK OK EMBL new in native format with EMBL CD-ROM index 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 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 configured databases |
Go to the output files for this example
Example 3
Display information on one explicit database:
% showdb -database tsw Displays information on configured 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 configured databases
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Example 5
Display protein databases only:
% showdb -nonucleic Displays information on configured databases # Name Type ID Qry All Comment # ============== ==== == === === ======= twp P OK OK OK EMBL new in native format with EMBL CD-ROM index 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 |
Example 6
Display the information with no headings:
% showdb -noheading Displays information on configured databases twp P OK OK OK EMBL new in native format with EMBL CD-ROM index 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 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 twp qapblast qapblastall qapblastsplit qapblastsplitexc qapblastsplitinc qapfasta qapflat qapflatall qapir qapirall qapirinc qapxfasta qapxflat qaxpir qaxpirall qaxpirinc tpir tsw tswnew 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 configured databases twp P 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 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 configured databases # Name Type ID Qry All Method Fields Defined Release Comment # ============== ==== == === === ========= ================= ======= ======= ======= twp P OK OK OK emblcd des global 16 EMBL new in native format with EMBL CD-ROM index 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 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 |
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 first file to standard output -filter boolean Read first file from standard input, write first file to 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)) |
# Name Type ID Qry All Comment # ============== ==== == === === ======= twp P OK OK OK EMBL new in native format with EMBL CD-ROM index 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 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.
EMBOSS provides excellent database support. All the common sequence formats you are likely to come across are supported. There are three basic levels of database query with different ways to search for and retrieve entries: entry A single entry specified by database ID or accession number is retrieved. For example "embl:x13776". query One or more entries matching a wildcard string in the USA are retrieved (this can be slow for some methods). For example you can specify all of the human PAX proteins in SWISS_PROT by: swissprot:pax*_human. all All entries are read sequentially from a database. For example to specify all entries in the database use embl:*.
One or more query levels may be available for a database depending on the database in question and how it has been setup and indexed. Each database and access method must be configured for it to be available for use. This involves editing one of the EMBOSS configuration files, either your own personal .embossrc or the installation-wide emboss.default file. The emboss.default file will typically contain the definitions of the test databases (tsw, tembl, tpir, etc) used in the usage examples for the application documentation and serve as example database definitions. For more information, see the EMBOSS Administrators Manual. You can run showdb to see the databases and access methods that have been configured successfully.
Where the string OK is given next to a database is listed in showdb output, this means showdb has read the database definition correctly and that this access method is in principle possible, in other words, the database has been configured correctly.. It does not mean that the database or access method are available or working correctly. You should check things are ok by running, for example, seqret to retrieve an entry.
Program name | Description |
---|---|
abiview | Display the trace in an ABI sequencer file |
cirdna | Draws circular maps of DNA constructs |
infoalign | Display basic information about a multiple sequence alignment |
infobase | Return information on a given nucleotide base |
inforesidue | Return information on a given amino acid residue |
infoseq | Display basic information about sequences |
lindna | Draws linear maps of DNA constructs |
pepnet | Draw a helical net for a protein sequence |
pepwheel | Draw a helical wheel diagram for a protein sequence |
prettyplot | Draw a sequence alignment with pretty formatting |
prettyseq | Write a nucleotide sequence and its translation to file |
remap | Display restriction enzyme binding sites in a nucleotide sequence |
seealso | Finds programs with similar function to a specified program |
showalign | Display a multiple sequence alignment in pretty format |
showfeat | Display features of a sequence in pretty format |
showseq | Displays sequences with features in pretty format |
sixpack | Display a DNA sequence with 6-frame translation and ORFs |
textsearch | Search the textual description of sequence(s) |
tfm | Displays full documentation for an application |
whichdb | Search all sequence databases for an entry and retrieve it |
wossname | Finds programs by keywords in their short description |