tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence

被引：9642

作者：

Lowe, TM ^{[1
]}

Eddy, SR ^{[1
]}

机构：

[1] WASHINGTON UNIV, SCH MED, DEPT GENET, ST LOUIS, MO 63110 USA

来源：

NUCLEIC ACIDS RESEARCH | 1997年 / 25卷 / 05期

关键词：

D O I：

10.1093/nar/25.5.955

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 [生物化学与分子生物学]; 081704 [应用化学];

摘要：

We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at similar to 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.

引用

页码：955 / 964

页数：10

共 36 条

[1]

ALTSCHUL SF, 1990, J MOL BIOL, V215, P403, DOI 10.1006/jmbi.1990.9999

[2]

THE ISOCHORE ORGANIZATION OF THE HUMAN GENOME AND ITS EVOLUTIONARY HISTORY - A REVIEW [J].

BERNARDI, G .

GENE, 1993, 135 (1-2) :57-66

[3]

DBEST - DATABASE FOR EXPRESSED SEQUENCE TAGS [J].

BOGUSKI, MS ;

LOWE, TMJ ;

TOLSTOSHEV, CM .

NATURE GENETICS, 1993, 4 (04) :332-333

[4]

Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii [J].

Bult, CJ ;

White, O ;

Olsen, GJ ;

Zhou, LX ;

Fleischmann, RD ;

Sutton, GG ;

Blake, JA ;

FitzGerald, LM ;

Clayton, RA ;

Gocayne, JD ;

Kerlavage, AR ;

Dougherty, BA ;

Tomb, JF ;

Adams, MD ;

Reich, CI ;

Overbeek, R ;

Kirkness, EF ;

Weinstock, KG ;

Merrick, JM ;

Glodek, A ;

Scott, JL ;

Geoghagen, NSM ;

Weidman, JF ;

Fuhrmann, JL ;

Nguyen, D ;

Utterback, TR ;

Kelley, JM ;

Peterson, JD ;

Sadow, PW ;

Hanna, MC ;

Cotton, MD ;

Roberts, KM ;

Hurst, MA ;

Kaine, BP ;

Borodovsky, M ;

Klenk, HP ;

Fraser, CM ;

Smith, HO ;

Woese, CR ;

Venter, JC .

SCIENCE, 1996, 273 (5278) :1058-1073

[5]

FINDING THE HAIRPIN IN THE HAYSTACK - SEARCHING FOR RNA MOTIFS [J].

DANDEKAR, T ;

HENTZE, MW .

TRENDS IN GENETICS, 1995, 11 (02) :45-50

[6]

REPEAT SEQUENCE FAMILIES DERIVED FROM MAMMALIAN TRANSFER-RNA GENES [J].

DANIELS, GR ;

DEININGER, PL .

NATURE, 1985, 317 (6040) :819-822

[7]

Deininger P.L., 1989, MOBILE DNA-UK, P619

[8]

RNA SEQUENCE-ANALYSIS USING COVARIANCE-MODELS [J].

EDDY, SR ;

DURBIN, R .

NUCLEIC ACIDS RESEARCH, 1994, 22 (11) :2079-2088

[9]

IDENTIFYING POTENTIAL TRANSFER-RNA GENES IN GENOMIC DNA-SEQUENCES [J].

FICHANT, GA ;

BURKS, C .

JOURNAL OF MOLECULAR BIOLOGY, 1991, 220 (03) :659-671

[10]

WHOLE-GENOME RANDOM SEQUENCING AND ASSEMBLY OF HAEMOPHILUS-INFLUENZAE RD [J].

FLEISCHMANN, RD ;

ADAMS, MD ;

WHITE, O ;

CLAYTON, RA ;

KIRKNESS, EF ;

KERLAVAGE, AR ;

BULT, CJ ;

TOMB, JF ;

DOUGHERTY, BA ;

MERRICK, JM ;

MCKENNEY, K ;

SUTTON, G ;

FITZHUGH, W ;

FIELDS, C ;

GOCAYNE, JD ;

SCOTT, J ;

SHIRLEY, R ;

LIU, LI ;

GLODEK, A ;

KELLEY, JM ;

WEIDMAN, JF ;

PHILLIPS, CA ;

SPRIGGS, T ;

HEDBLOM, E ;

COTTON, MD ;

UTTERBACK, TR ;

HANNA, MC ;

NGUYEN, DT ;

SAUDEK, DM ;

BRANDON, RC ;

FINE, LD ;

FRITCHMAN, JL ;

FUHRMANN, JL ;

GEOGHAGEN, NSM ;

GNEHM, CL ;

MCDONALD, LA ;

SMALL, KV ;

FRASER, CM ;

SMITH, HO ;

VENTER, JC .

SCIENCE, 1995, 269 (5223) :496-512

← 1 2 3 4 →