Biopolym. Cell. 1990; 6(6):42-48.
A method for search of structure motifs in amlnoacid sequences program site of the GenBee package
1, 2Koonin E. V., 2Chumakov K. M., 2Gorbalenya A. E.
  1. Institute of Microbiology, Academy of Sciences of the USSR
    Moscow, USSR
  2. Institute of Poliomyelitis and Viral Encephalitides, Academy of Medical Sciences of the USSR
    Moscow Region, USSR


A method is suggested to search for the structure motifs in amino acid sequences, based on their scanning by frequency profiles generated from aligned sequence segments. The program «SITE» implementing the proposed algorithm is discussed, exemplified by the search of an amino acid sequence database for the motif typical of a vast class of purine NTP-binding proteins. The superiorities of the proposed approach as compared to standard pattern-searching routines is demonstrated with respect to selectivity and completeness of extraction of relevant sequences.


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