Protein sequence motif derivation with extreme sensitivity
Alexander Goncearenco (developed in 2007-2012 at the University of Bergen, Norway)
Designed to derive sequence motifs of elementary functional loops (EFL) in proteins.
Supports MPI parallelization.
The package contains:
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converge - find conserved motifs in sequence
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clustering - reduce the number of derived motifs by combining the similar ones
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search - find matches of a predefined motif in sequece database
Utilities:
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findPermutatons.R - find positional permutations that destroy relative positional distances and hence the natural motif
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convertMSA.pl - convert multiple sequence alignment to initial motif
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composition.csv - average prokaryotic proteomic composition
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profile_logo.py - generate profile logo graphics
Check other branches as well for modifications.