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From CAGT

ATTCREPCGAGFINDTTAA

REPFIND is a program to find clustered, exact repeats in nucleotide sequences. For each repeat cluster that it finds, it calculates a P-value, which indicates the probability of finding such a concentration of that particular repeat just by chance. Of the many possible clusters for each repeated word, REPFIND selects the one with the most significant P-value.

We are using REPFIND to study localization of messenger RNAs. These molecules sometimes contain signals in their 3' untranslated regions that specify how they are transported in the cell, prior to being translated. This process is essential for establishing body axes in embryogenesis, among other things. The localization signals often appear to consist of repeat clusters that can be detected by REPFIND.

Publication: JN Betley, MC Frith, JH Graber, S Choo, JO Deshler (2002). A ubiquitous and conserved signal for RNA localization in chordates. Current Biology, 12, 1756-61.

Protein Engineering