SWISSPROT [Bairoch and Apweiler, 1999] is a manually curated protein sequence database that provides high quality annotation. TrEMBL [Bairoch and Apweiler, 1999] is a manually checked translation of the EMBL database [Stoesser et al.,1999] to complement the SWISSPROT database. Data is added to TrEMBL faster than that it could be manually annotated. Currently position independent annotation is added to TrEMBL automatically by a process called distributed annotation [Moeller et al., 1999].
Position specific SWISSPROT annotation can be copied by similarity. The featurePropagation package allows controlled propagation of these position specific features to other entries. It uses an alignment of a master entry and a set of target entries. This alignment is made using either CLUSTALW [Thompson et al., 1994] or FASTA [Pearson, 1990]. The alignment is used for positioning the master features on the target sequence and for calculating the score of each individual feature.
The copying process is controlled by a set of rules. These rules describe the features and can set thresholds for feature similarity (local), protein similarity (global) or check for a pattern in the target protein sequence. The newly created feature lines are tagged with master entry details for future referencing.
The program is written in JAVA and is usable on most platforms. It is used for annotating TrEMBL and for
doing curator controlled bulk annotation in SWISSPROT.
The featurePropagation package is available on request. Contact avelds@ebi.ac.uk
.
The package is largely build upon the SWISS package by S. Möller (moeller@ebi.ac.uk ). The SWISS package is a set of JAVA classes that provide reading, modifying and writing functionality for SWISSPROT formatted entries.