Exercise: showdb

As an example, here are the first few databases available using EMBOSS at the HGMP. Your local site will probably have a different selection of databases depending on what the local EMBOSS maintainer has set up.

unix % showdb
Displays information on the currently available databases

#Name	Type	ID	Qry	All	Comment
#====	====	==	===	===	=======
nbrf	P	OK	OK	OK	PIR/NBRF
pir	P	OK	OK	OK	PIR/NBRF
remtrtembl	P	OK	OK	OK	REMTRtembl sequences
sptrtembl	P	OK	OK	OK	SPTRtembl sequences
sw	P	OK	OK	OK	SWISSPROT sequences
swissprot	P	OK	OK	OK	SWISSPROT sequences
trarc	P	OK	OK	OK	TRtembl ARC sequences
trtembl	P	OK	OK	OK	TRtembl sequences
trtemblnew	P	OK	OK	OK	New TRtembl sequences

showdb writes out a simple table displaying the names, contents and access methods for the databases.

ID allows programs to extract a single explicitly named entry from the database, for example: tembl:x13776

Query indicates that programs can extract a set of matching wildcard entry names. For example: swissprot:pax*_human

All allows programs to analyse all the entries in the database sequentially. For example: tembl:*

You can access tembl by either identifier eg xlrhodop, or accession number eg L07770. Let's try these now.