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Nucleic Acids Research, 1992, Vol. 20, No. 11 2717-2724
© 1992

MOLECULAR BIOLOGY

Computer methods for locating kinetoplastid cryptogenes

Arndt von Haeseler1, Beat Blum2, Larry Simpson2, Nancy Sturm2 and Michael S. Waterman1,3,*

1Department of Mathematics, University of Southern California Los Angeles, CA 90089-1113 2Department of Biology, University of California Los Angeles, CA 90024 3Department of Molecular Biology, University of Southern California Los Angeles, CA 90089-1340, USA

*To whom correspondence should be addressed at: Department of Mathematics. University of Southern California, Los Angeles. CA 90089-1113, USA

Received March 18, 1992. Revised April 7, 1992. Accepted April 7, 1992.

RNA editing in the mitochondria of kinetoplastid protoza Involves the insertion and/or deletion of precise numbers of uridine residues at precise locations in the transcribed RNA of certain genes. These genes are known as cryptogenes. In this paper we study computational algorithms to search for unknown cryptogenes and for the associated templates for insertion of uridines, gRNA sequences. The pairwise similarity search algorithm of Smith and Waterman (1) is modified to study this problem. The algorithm searches for unknown gRNAs given the cryptogene sequence. The method is tested on 4 known cryptogenes from L.tarentolse which are known to have 7 associated gRNAs. The statistical distribution of the longest gRNA when comparing random sequences is derived. Finally we develop an algorithm to search for cryptogenes using amino acid sequences from related proteins.


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