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
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.
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