Database access modes

EMBOSS offers three modes for accessing databases:

Single:

EMBOSS retrieves a single sequence indexed by ID.

Query:

EMBOSS retrieves a set of sequences corresponding to a query that can return more than one entry, including accession numbers or wildcard IDs.

All:

EMBOSS returns all the sequences in the database in no particular order.

Each database definition can configure one or many of these modes for database access.

Typically EMBOSS uses variations on the emblcd system of database indexing to provide rapid access in single and query modes to flat file databases. The emblcd method is implemented in a variety of ways depending on the original format of your database. The emblcd method assumes that you have one or both of ID and accession number in each record and that they are unique for the whole database index. EMBOSS also provides methods for retrieving sequences via the WWW and three specific methods for interaction with SRS http://www.lionbioscience.com/solutions/srs installed localy or through a remote public server. For other non flatfile databases or flat file databases in formats not currently supported by EMBOSS you will have to configure an external application to retrieve sequences.