A computer program for aligning a cDNA sequence with a genomic DNA sequence

被引：559

作者：

Florea, L

Hartzell, G

Zhang, Z

Rubin, GM

Miller, W ^{[1
]}

机构：

[1] Penn State Univ, Dept Comp Engn & Sci, University Pk, PA 16802 USA

[2] Drosophila Genome Ctr, Berkeley, CA 94720 USA

来源：

GENOME RESEARCH | 1998年 / 8卷 / 09期

关键词：

D O I：

10.1101/gr.8.9.967

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：

We address the problem of efficiently aligning a transcribed and spliced DNA sequence with a genomic sequence containing that gene, allowing for introns in the genomic sequence and a relatively small number of sequencing errors. A freely available computer program, described herein, solves the problem for a 100-kb genomic sequence in a few seconds on a workstation.

引用

页码：967 / 974

页数：8

共 27 条

[1] BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[2]

Ansari-Lari MA, 1998, GENOME RES, V8, P29

[3] Large-scale sequencing in human chromosome 12p13: Experimental and computational gene structure determination [J].

AnsariLari, MA ;

Shen, Y ;

Muzny, DM ;

Lee, W ;

Gibbs, RA .

GENOME RESEARCH, 1997, 7 (03) :268-280

[4] Analysis of EST-driven gene annotation in human genomic sequence [J].

Bailey, LC ;

Searls, DB ;

Overton, GC .

GENOME RESEARCH, 1998, 8 (04) :362-376

[5]

Birney E, 1997, ISMB-97 - FIFTH INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY, PROCEEDINGS, P56

[6] DBEST - DATABASE FOR EXPRESSED SEQUENCE TAGS [J].

BOGUSKI, MS ;

LOWE, TMJ ;

TOLSTOSHEV, CM .

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

[7] Prediction of complete gene structures in human genomic DNA [J].

Burge, C ;

Karlin, S .

JOURNAL OF MOLECULAR BIOLOGY, 1997, 268 (01) :78-94

[8]

Chao KM, 1997, COMPUT APPL BIOSCI, V13, P75

[9] SGD:: Saccharomyces Genome Database [J].

Cherry, JM ;

Adler, C ;

Ball, C ;

Chervitz, SA ;

Dwight, SS ;

Hester, ET ;

Jia, YK ;

Juvik, G ;

Roe, T ;

Schroeder, M ;

Weng, SA ;

Botstein, D .

NUCLEIC ACIDS RESEARCH, 1998, 26 (01) :73-79

[10]

EDDY SR, 1994, ADV MOL PLANT NEMATO, P3

← 1 2 3 →