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.
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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: 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.