Recognition of genes in human DNA sequences

被引：12

作者：

Gelfand, MS ^{[1
]}

Podolsky, LI ^{[1
]}

Astakhova, TV ^{[1
]}

Roytberg, MA ^{[1
]}

机构：

[1] RUSSIAN ACAD SCI,INST MATH PROBLEMS BIOL,PUSHCHINO 142292,RUSSIA

来源：

JOURNAL OF COMPUTATIONAL BIOLOGY | 1996年 / 3卷 / 02期

关键词：

exon-intron structure; gene recognition; exons; multicriterial optimization; Pareto set;

D O I：

10.1089/cmb.1996.3.223

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A new approach to computer-assisted gene recognition in higher eukaryote DNA is suggested, It allows one to use not only linear functions for scoring structures, but all functions satisfying natural monotonicity conditions, The algorithm constructs the set of structures guaranteed to contain an optimal structure for every function, So, it uncouples the time-consuming step of generation of this set from the fast step of structure scoring, thus making it simple to experiment with different functions, One particular scoring function, taking into account only codon usage and positional nucleotide frequencies of the splicing sites, has been implemented in the Genome Recognition and Exon Assembly Tool program, and has been tested on an independent sample of human genes, yielding 88% sensitivity and 79% specificity.

引用

页码：223 / 234

页数：12

共 22 条

[1]

[Anonymous], P 2 INT C BIOINF SUP

[2] SELECTION OF DNA-BINDING SITES BY REGULATORY PROTEINS - STATISTICAL-MECHANICAL THEORY AND APPLICATION TO OPERATORS AND PROMOTERS [J].

BERG, OG ;

VONHIPPEL, PH .

JOURNAL OF MOLECULAR BIOLOGY, 1987, 193 (04) :723-743

[3] GENE STRUCTURE PREDICTION BY LINGUISTIC METHODS [J].

DONG, S ;

SEARLS, DB .

GENOMICS, 1994, 23 (03) :540-551

[4] ASSESSMENT OF PROTEIN CODING MEASURES [J].

FICKETT, JW ;

TUNG, CS .

NUCLEIC ACIDS RESEARCH, 1992, 20 (24) :6441-6450

[5]

FIELDS CA, 1990, COMPUT APPL BIOSCI, V6, P263

[6] COMPUTATION OF BIOPOLYMERS - A GENERAL-APPROACH TO DIFFERENT PROBLEMS [J].

FINKELSTEIN, AV ;

ROYTBERG, MA .

BIOSYSTEMS, 1993, 30 (1-3) :1-19

[7]

Gelfand M S, 1995, J Comput Biol, V2, P87, DOI 10.1089/cmb.1995.2.87

[8] PREDICTION OF THE EXON-INTRON STRUCTURE BY A DYNAMIC-PROGRAMMING APPROACH [J].

GELFAND, MS ;

ROYTBERG, MA .

BIOSYSTEMS, 1993, 30 (1-3) :173-182

[9] STATISTICAL-ANALYSIS OF MAMMALIAN PRE-MESSENGER RNA SPLICING SITES [J].

GELFAND, MS .

NUCLEIC ACIDS RESEARCH, 1989, 17 (15) :6369-6382

[10] COMPUTER-PREDICTION OF THE EXON-INTRON STRUCTURE OF MAMMALIAN PRE-MESSENGER-RNAS [J].

GELFAND, MS .

NUCLEIC ACIDS RESEARCH, 1990, 18 (19) :5865-5869

← 1 2 3 →