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showdb |
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.
Display information on the currently available databases:
% showdb Displays information on the currently available databases # Name Type ID Qry All Comment # ==== ==== == === === ======= enspep P OK OK OK ENSEMBL pep enspepp P OK OK OK ENSEMBL pep predicted enspeppredicted P OK OK OK ENSEMBL pep predicted remtrembl P OK OK OK REMTREMBL sequences sptrembl P OK OK OK SPTREMBL sequences sw P OK OK OK SWISSPROT sequences swissprot P OK OK OK SWISSPROT sequences tpir P OK OK OK PIR using NBRF access for 4 files trembl P OK OK OK TREMBL sequences tsw P OK OK OK Swissprot native format with EMBL CD-ROM index tswnew P OK OK OK Swissnew 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 em N OK OK OK EMBL sequences embl N OK OK OK EMBL sequences emblnew N OK OK OK New EMBL sequences enscdna N OK OK OK ENSEMBL cdna ensdna N OK OK OK ENSEMBL dna ensdnam N OK OK OK ENSEMBL dna masked ensdnamasked N OK OK OK ENSEMBL dna masked ensembl N OK OK OK ENSEMBL est N OK OK OK EMBL EST sequences fungal N OK OK OK EMBL fungal sequences gb N OK OK OK Genbank updates genbank N OK OK OK Genbank gss N OK OK OK EMBL GSS sequences hsunigene N OK - - hsunigene htg N OK OK OK EMBL HTG sequences human N OK OK OK EMBL human sequences humanest N OK OK OK EMBL human EST sequences invertebrate N OK OK OK EMBL invertebrate sequences mammalian N OK OK OK EMBL mammalian sequences mouseest N OK OK OK EMBL mouse EST sequences newgb N OK OK OK Genbank updates newgenbank N OK OK OK Genbank updates organelle N OK OK OK EMBL organelle sequences otherest N OK OK OK EMBL other EST sequences othervertebrate N OK OK OK EMBL other vertebrate sequences patent N OK OK OK EMBL patented sequences phage N OK OK OK EMBL phage sequences plant N OK OK OK EMBL plant sequences prokaryotic N OK OK OK EMBL prokaryotic sequences refseq N OK OK OK REFSEQ sequences with features in /home/br2/data/Chris... refseq_srs N OK - - REFSEQ-ID sequences from SRS rodent N OK OK OK EMBL rodent sequences sts N OK OK OK EMBL STS sequences synthetic N OK OK OK EMBL synthetic sequences tembl N OK OK OK EMBL in native format with EMBL CD-ROM index tgb N OK - - Genbank IDs tgenbank N OK OK OK GenBank in native format with EMBL CD-ROM index tigregad N OK OK OK TIGR EGAD sequences tigrmgi N OK OK OK TIGR MGI sequences unclassified N OK OK OK EMBL unclassified sequences vertebrate N OK OK OK EMBL vertebrate sequences viral N OK OK OK EMBL viral sequences |
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
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Example 5
Display protein databases only:
% showdb -nonucleic Displays information on the currently available databases # Name Type ID Qry All Comment # ==== ==== == === === ======= enspep P OK OK OK ENSEMBL pep enspepp P OK OK OK ENSEMBL pep predicted enspeppredicted P OK OK OK ENSEMBL pep predicted remtrembl P OK OK OK REMTREMBL sequences sptrembl P OK OK OK SPTREMBL sequences sw P OK OK OK SWISSPROT sequences swissprot P OK OK OK SWISSPROT sequences tpir P OK OK OK PIR using NBRF access for 4 files trembl P OK OK OK TREMBL sequences tsw P OK OK OK Swissprot native format with EMBL CD-ROM index tswnew P OK OK OK Swissnew 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 enspep P OK OK OK ENSEMBL pep enspepp P OK OK OK ENSEMBL pep predicted enspeppredicted P OK OK OK ENSEMBL pep predicted remtrembl P OK OK OK REMTREMBL sequences sptrembl P OK OK OK SPTREMBL sequences sw P OK OK OK SWISSPROT sequences swissprot P OK OK OK SWISSPROT sequences tpir P OK OK OK PIR using NBRF access for 4 files trembl P OK OK OK TREMBL sequences tsw P OK OK OK Swissprot native format with EMBL CD-ROM index tswnew P OK OK OK Swissnew 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 em N OK OK OK EMBL sequences embl N OK OK OK EMBL sequences emblnew N OK OK OK New EMBL sequences enscdna N OK OK OK ENSEMBL cdna ensdna N OK OK OK ENSEMBL dna ensdnam N OK OK OK ENSEMBL dna masked ensdnamasked N OK OK OK ENSEMBL dna masked ensembl N OK OK OK ENSEMBL est N OK OK OK EMBL EST sequences fungal N OK OK OK EMBL fungal sequences gb N OK OK OK Genbank updates genbank N OK OK OK Genbank gss N OK OK OK EMBL GSS sequences hsunigene N OK - - hsunigene htg N OK OK OK EMBL HTG sequences human N OK OK OK EMBL human sequences humanest N OK OK OK EMBL human EST sequences invertebrate N OK OK OK EMBL invertebrate sequences mammalian N OK OK OK EMBL mammalian sequences mouseest N OK OK OK EMBL mouse EST sequences newgb N OK OK OK Genbank updates newgenbank N OK OK OK Genbank updates organelle N OK OK OK EMBL organelle sequences otherest N OK OK OK EMBL other EST sequences othervertebrate N OK OK OK EMBL other vertebrate sequences patent N OK OK OK EMBL patented sequences phage N OK OK OK EMBL phage sequences plant N OK OK OK EMBL plant sequences prokaryotic N OK OK OK EMBL prokaryotic sequences refseq N OK OK OK REFSEQ sequences with features in /home/br2/data/Chris... refseq_srs N OK - - REFSEQ-ID sequences from SRS rodent N OK OK OK EMBL rodent sequences sts N OK OK OK EMBL STS sequences synthetic N OK OK OK EMBL synthetic sequences tembl N OK OK OK EMBL in native format with EMBL CD-ROM index tgb N OK - - Genbank IDs tgenbank N OK OK OK GenBank in native format with EMBL CD-ROM index tigregad N OK OK OK TIGR EGAD sequences tigrmgi N OK OK OK TIGR MGI sequences unclassified N OK OK OK EMBL unclassified sequences vertebrate N OK OK OK EMBL vertebrate sequences viral N OK OK OK EMBL viral sequences |
Example 7
Display just a list of the available database names:
% showdb -noheading -notype -noid -noquery -noall -nocomment -auto enspep enspepp enspeppredicted remtrembl sptrembl sw swissprot tpir trembl tsw tswnew twp em embl emblnew enscdna ensdna ensdnam ensdnamasked ensembl est fungal gb genbank gss hsunigene htg human humanest invertebrate mammalian mouseest newgb newgenbank organelle otherest othervertebrate patent phage plant prokaryotic refseq refseq_srs rodent sts synthetic tembl tgb tgenbank tigregad tigrmgi unclassified vertebrate viral |
Example 8
Display only the names and types:
% showdb -only -type Displays information on the currently available databases enspep P enspepp P enspeppredicted P remtrembl P sptrembl P sw P swissprot P tpir P trembl P tsw P tswnew P twp P em N embl N emblnew N enscdna N ensdna N ensdnam N ensdnamasked N ensembl N est N fungal N gb N genbank N gss N hsunigene N htg N human N humanest N invertebrate N mammalian N mouseest N newgb N newgenbank N organelle N otherest N othervertebrate N patent N phage N plant N prokaryotic N refseq N refseq_srs N rodent N sts N synthetic N tembl N tgb N tgenbank N tigregad N tigrmgi N unclassified N vertebrate N viral N |
Standard (Mandatory) qualifiers: (none)
Additional (Optional) qualifiers:
-database string Name of a single database to give
information on
-html boolean Format output as an HTML table
-[no]protein boolean Display protein databases
-[no]nucleic boolean Display nucleic acid databases
-fields boolean This displays the search fields that can be
used on this database, other than the
standard 'id' or 'acc' fields.
-release boolean Display 'release' column
-outfile outfile Output file name
Advanced (Unprompted) qualifiers:
-only boolean This is a way of shortening the command line
if you only want a few things to be
displayed. Instead of specifying:
'-nohead -notype -noid -noquery -noall'
to get only the comment output, you can
specify
'-only -comment'
-heading boolean Display column headings
-type boolean Display 'type' column
-id boolean Display 'id' column
-query boolean Display 'qry' column
-all boolean Display 'all' column
-comment boolean 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 deaths
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| 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 |
| -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 | No |
| -release | Display 'release' column | Boolean value Yes/No | No |
| -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 things to be displayed. Instead of specifying: '-nohead -notype -noid -noquery -noall' to get only the comment output, you can specify '-only -comment' | Boolean 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 # ==== ==== == === === ======= enspep P OK OK OK ENSEMBL pep enspepp P OK OK OK ENSEMBL pep predicted enspeppredicted P OK OK OK ENSEMBL pep predicted remtrembl P OK OK OK REMTREMBL sequences sptrembl P OK OK OK SPTREMBL sequences sw P OK OK OK SWISSPROT sequences swissprot P OK OK OK SWISSPROT sequences tpir P OK OK OK PIR using NBRF access for 4 files trembl P OK OK OK TREMBL sequences tsw P OK OK OK Swissprot native format with EMBL CD-ROM index tswnew P OK OK OK Swissnew 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 em N OK OK OK EMBL sequences embl N OK OK OK EMBL sequences emblnew N OK OK OK New EMBL sequences enscdna N OK OK OK ENSEMBL cdna ensdna N OK OK OK ENSEMBL dna ensdnam N OK OK OK ENSEMBL dna masked ensdnamasked N OK OK OK ENSEMBL dna masked ensembl N OK OK OK ENSEMBL est N OK OK OK EMBL EST sequences fungal N OK OK OK EMBL fungal sequences gb N OK OK OK Genbank updates genbank N OK OK OK Genbank gss N OK OK OK EMBL GSS sequences hsunigene N OK - - hsunigene htg N OK OK OK EMBL HTG sequences human N OK OK OK EMBL human sequences humanest N OK OK OK EMBL human EST sequences invertebrate N OK OK OK EMBL invertebrate sequences mammalian N OK OK OK EMBL mammalian sequences mouseest N OK OK OK EMBL mouse EST sequences newgb N OK OK OK Genbank updates newgenbank N OK OK OK Genbank updates organelle N OK OK OK EMBL organelle sequences otherest N OK OK OK EMBL other EST sequences othervertebrate N OK OK OK EMBL other vertebrate sequences patent N OK OK OK EMBL patented sequences phage N OK OK OK EMBL phage sequences plant N OK OK OK EMBL plant sequences prokaryotic N OK OK OK EMBL prokaryotic sequences refseq N OK OK OK REFSEQ sequences with features in /home/br2/data/Chris... refseq_srs N OK - - REFSEQ-ID sequences from SRS rodent N OK OK OK EMBL rodent sequences sts N OK OK OK EMBL STS sequences synthetic N OK OK OK EMBL synthetic sequences tembl N OK OK OK EMBL in native format with EMBL CD-ROM index tgb N OK - - Genbank IDs tgenbank N OK OK OK GenBank in native format with EMBL CD-ROM index tigregad N OK OK OK TIGR EGAD sequences tigrmgi N OK OK OK TIGR MGI sequences unclassified N OK OK OK EMBL unclassified sequences vertebrate N OK OK OK EMBL vertebrate sequences viral N OK OK OK EMBL viral sequences |
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.
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: Doc/Admin_guide/adminguide/ especially: Doc/Admin_guide/adminguide/node4.html
See also: Usa/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.
| 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 a sequence with restriction cut 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 text. SRS and Entrez are faster! |
| 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 |