EMOTIF 3.6 – Sequence Analysis Using Pareto-optimal Discrete Motifs



EMOTIF includes the following three programs:

(1) eMOTIF-SEARCH: Given a protein sequence, the eMOTIF-SEARCH program suggests families of proteins to which the query sequence may belong. The eMOTIF-SEARCH program considers a protein sequence a potential member of a protein family, if the sequence contains discrete motif or motifs that have been generated from an ungapped multiple sequence alignment of known member sequences from that family.

(2) eMOTIF-MAKER: The eMOTIF-MAKER program converts an ungapped multiple sequence alignment into a set of Pareto-optimal discrete motifs for use by the eMOTIF-SEARCH program and the eMOTIF-SCAN program. The resulting set of motifs often reveals sub-families within the cluster of proteins that share the region of sequence similarity covered by the given ungapped multiple sequence alignment.

(3) eMOTIF-SCAN: Given a regular expression, the eMOTIF-SCAN program finds all the occurrences of that regular expression in a particular sequence database.


 The Brutlag Bioinformatics Group




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Nevill-Manning, C. G., Wu, T. D. and Brutlag, D. L. (1998).
Highly Specific Protein Sequence Motifs for Genome Analysis.
Proc. Natl. Acad. Sci. May 26, 1998 vol. 95 no. 11 5865-5871

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