Related web sites

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• MEME is the motif discovery tool that builds the motif models that serve as input to Meta-MEME. MEME can be used to find motifs in DNA or protein sequences.


• MAST is a database search tool that uses multiple MEME motif models to search a protein or DNA database. MAST differs from Meta-MEME in that MAST treats each motif model independently, rather than combining the motif models into a single meta-model.


• SAM is a hidden Markov model toolkit, developed at the University of California, Santa Cruz. Unlike Meta-MEME, SAM models are not motif-based. However, SAM supports both DNA and protein models.


• HMMER is another hidden Markov model toolkit. Developed by Sean Eddy at Washington University in St. Louis, the HMMER toolkit includes a number of homology detection programs for specific tasks. These can be used with Meta-MEME by converting linear Meta-MEME models into HMMER version 1.8 models.


• The BLOCKS database is a searchable collection of PROSITE motifs. The associated BLOCKMAKER software allows for the construction of new motif blocks.


• Pfam is a database of protein domain multiple alignments and HMMs.

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Please send comments and questions to Charles Grant at cegrant@u.washington.edu.