Computer methods for locating kinetoplastid cryptogenes.

von Haeseler A, Blum B, Simpson L, Sturm N, Waterman MS
Nucleic Acids Res. 1992 20 (11): 2717-24

PMID: 1614859 · PMCID: PMC336913 · DOI:10.1093/nar/20.11.2717

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 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.tarentolae 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.

MeSH Terms (9)

Algorithms Amino Acid Sequence Animals Base Sequence DNA, Mitochondrial Genes Leishmania Molecular Sequence Data Sequence Alignment

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