mmsearch: a motif arrangement language and search program

This paper presents a language for describing arrangements of motifs in biological sequences, and a program that uses the language to find the arrangements in motif match databases. The program does not by itself search for the constituent motifs, and is thus independent of how they are detected, which allows it to use motif match data of various origins. AVAILABILITY: The program can be tested online at and the distribution is available from CONTACT: SUPPLEMENTARY INFORMATION: The full documentation about mmsearchis available from

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