COMPUTER METHODS FOR LOCATING KINETOPLASTID CRYPTOGENES

被引:14
作者
VONHAESELER, A
BLUM, B
SIMPSON, L
STURM, N
WATERMAN, MS
机构
[1] UNIV SO CALIF,DEPT MATH,LOS ANGELES,CA 90089
[2] UNIV CALIF LOS ANGELES,DEPT BIOL,LOS ANGELES,CA 90024
[3] UNIV SO CALIF,DEPT MOLEC BIOL,LOS ANGELES,CA 90089
基金
美国国家科学基金会; 美国国家卫生研究院;
关键词
D O I
10.1093/nar/20.11.2717
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.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.
引用
收藏
页码:2717 / 2724
页数:8
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