Sequence Motif Search Program

MRC Laboratory of Molecular Biology, Hills Road, Cambridge - CB2 2QH, United Kingdom
Phone: +44-(0)1223-402043 :: Fax: +44-(0)1223-213556


Harvey McMahon's Group Page




This program allows the user to search for multiple occurrences of short amino acid motifs in a chosen genome or for the co-occurrences of multiple motifs. The program also gives the expected number of sequences to have the motif occurring multiple times using the observed length and amino acid distribution in the sequences for each genome.



Please enter the first sequence motif here:

Usage/Pattern representation:

  • To represent any aminoacid, use the alphabet 'X'. e.g. DXF means D followed by any aminoacid followed by F
  • To represent a set of amino acids in a particular position, enclose the set within parantheses '[ ]'. e.g. D[AILPNS]F means D followed by one of the amino acids in the set [AILPNS] followed by F
  • To represent a bulky hydrophobic residue, use the character 5. e.g. YXX5 means Y followed by any two amino acids followed by one of the amino acids in the set [VFILMW]
  • To exclude an aminoacid, use the ^ symbol within '[ ]'. e.g. F[^P]R means F followed by any aminoacid but Proline followed by R
  • To exclude more than one aminoacid in a position, use the ^ symbol and enclose all aminoacids to be excluded in '[ ]' for that position. e.g. G[^EDKRH]L means G followed by any aminoacid but E,D,R,K,H followed by L

Please choose the organism:

Human  Mouse  Danio rerio  Anopheles  Worm  Fly  Yeast  Dicty  Trypanosome 






This page is maintained by M. Madan Babu for Dr. Harvey McMahon - MRC Laboratory of Molecular Biology, Hills Road, Cambridge - CB22QH, UK

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Since 1st Aug 2002