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The program Matcher
was developed to analyze whether a protein
(or DNA sequence) contains a periodically repeated pattern of amino
acids (or nucleotides). It has been adapted to be used to determine whether
a given protein contains the
7 residue periodicity
associated with coiled-coil proteins. The
program can be used to give the periodic alignment of a given protein,
or be used to analyze an entire file of amino acid sequences. In the
latter case, the program will first rank the sequences with respect to
their potential alignment to
, without giving
the alignment.
References: V.A. Fischetti, G.M. Landau, J.P. Schmidt, P. Sellers, ``Identifying periodic occurrences of a template with applications to protein structure,'' Information Processing Letters 45, pp. 11-18, 1993. V. Fischetti, V. Pancholi, P. Sellers, J. Schmidt, G. Landau, X. Xu, O. Schneewind, ``Streptococcal M protein: A common structural motif used by Gram-positive bacteria for biological active surface molecules,'' Molecular Recognition in Host-Parasite Interactions: Mechanisms in viral, bacterial and parasite infections, Published by Plenum Publishing, in print. You can run Matcher from this page or download matcher to your machine. For additional features, you can download a postscript version of the manual.
To run Matcher, type in or paste your protein sequence in the
sequence window below. You may also type in a title for the sequence
(optional). Press the align button and Matcher will
align your sequence.
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