eMATRIX 2.0 – Fast Probabilistic Analysis of Sequence Function using Scoring Matrices



eMATRIX performs the following functions:

(1) EMATRIX-SEARCH: EMATRIX-SEARCH determines the function of a sequence. Given a protein sequence, EMATRIX-SEARCH identifies the sequence by finding matches with a precompiled database of scoring matrices. The scoring matrices are generated by the EMATRIX-MAKER program for each alignment block in a given database, such as BLOCKSPLUS. EMATRIX-SEARCH has been optimized for speed, and can be used for genome-wide functional analysis.

(2) EMATRIX-MAKER: EMATRIX-MAKER converts an alignment block into a minimal-risk scoring matrix, for use in sequence analysis. EMATRIX-MAKER is used primarily in batch mode to construct the databases for the EMATRIX-SEARCH program. However, the EMATRIX-MAKER program can also be used to convert an individual alignment block into a scoring matrix. That scoring matrix can then be used by EMATRIX-SCAN program to scan a sequence database for homologs.

(3) EMATRIX-SCAN: EMATRIX-SCAN searches a sequence database for sequences that match a given scoring matrix. Such a scoring matrix might be generated by EMATRIX-MAKER.


 The Brutlag Bioinformatics Group




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Wu, T. D., Nevill-Manning, C. G. and Brutlag, D. L. (2000).
Fast probabilistic analysis of sequence function using scoring matrices.
Bioinformatics, 16, 1-12.