Protein Sequence Motifs

We analyse consensus predicted epitopes (and flanking sequences) for the presence of protein sequence motifs contained in the PROSITE database. This analysis is performed from within BIOVIA (formerly Accelrys) Discovery Studio software, for a maximum of 4 consensus predicted epitopes.

PROSITE contains structural and functional patterns found within protein sequences. The database is produced and maintained by ExPaSy, Switzerland.

A motif in the PROSITE database is described either as a PATTERN or a MATRIX. PATTERNS are published motifs that have been tested against the SWISSPROT protein database for specificity to a group or family of proteins.

A MATRIX is a table of position specific amino acid weights and gap costs. The numbers are used to calculate a similarity score for an alignment between any sequence and profile. An alignment with a score that is higher than or equal to a predetermined cut-off value is considered to be a motif sequence

Reference
Hulo N., Bairoch A., Bulliard V., Cerutti L., Cuche B., De Castro E., Lachaize C., Langendijk-Genevaux P.S., Sigrist C.J.A.
The 20 years of PROSITE. Nucleic Acids Res. 2007 Nov 14.
PubMed: 18003654 [Full text] [PDF version]

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