THOR: targeted high-throughput ortholog reconstructor

被引：5

作者：

Bainbridge, Matthew N. ^{[1
]}

Warren, Rene L. ^{[1
]}

He, An ^{[1
]}

Bilenky, Mikhail ^{[1
]}

Robertson, A. Gordon ^{[1
]}

Jones, Steven J. M. ^{[1
]}

机构：

[1] British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC, Canada

来源：

BIOINFORMATICS | 2007年 / 23卷 / 19期

关键词：

D O I：

10.1093/bioinformatics/btl513

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Low-coverage genomes (LCGs) are becoming an increasingly important source of data for phylogenitic studies. However, assembly of these genomes is time consuming, difficult and lags behind sequence genaration. THOR is a fast, stringent application for targeted reconstruction of sequence orthlogs inunassembled LCGs. Using a 4x coverage set of mouse whole-genome sequence reads, THOR could partially or completely reconstruct 416/1000 human promoter ortholog regions in similar to 7.3 min/promoter. THOR's reconstruction rate improves markedly with both higher-coverage, and less divergent target species.

引用

页码：2622 / 2624

页数：3

共 7 条

[1] Distribution and intensity of constraint in mammalian genomic sequence [J].

Cooper, GM ;

Stone, EA ;

Asimenos, G ;

Green, ED ;

Batzoglou, S ;

Sidow, A .

GENOME RESEARCH, 2005, 15 (07) :901-913

[2] Characterization of evolutionary rates and constraints in three mammalian genomes [J].

Cooper, GM ;

Brudno, M ;

Stone, EA ;

Dubchak, I ;

Batzoglou, S ;

Sidow, A .

GENOME RESEARCH, 2004, 14 (04) :539-548

[3] An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing [J].

Margulies, EH ;

Vinson, JP ;

Miller, W ;

Jaffe, DB ;

Lindblad-Toh, K ;

Chang, JL ;

Green, ED ;

Lander, ES ;

Mullikin, JC ;

Clamp, M .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (13) :4795-4800

[4] Comparative genome assembly [J].

Pop, M ;

Phillippy, A ;

Delcher, AL ;

Salzberg, SL .

BRIEFINGS IN BIOINFORMATICS, 2004, 5 (03) :237-248

[5] cisRED: a database system for genome-scale computational discovery of regulatory elements [J].

Robertson, G. ;

Bilenky, M. ;

Lin, K. ;

He, A. ;

Yuen, W. ;

Dagpinar, M. ;

Varhol, R. ;

Teague, K. ;

Griffith, O. L. ;

Zhang, X. ;

Pan, Y. ;

Hassel, M. ;

Sleumer, M. C. ;

Pan, W. ;

Pleasance, E. D. ;

Chuang, M. ;

Hao, H. ;

Li, Y. Y. ;

Robertson, N. ;

Fjell, C. ;

Li, B. ;

Montgomery, S. B. ;

Astakhova, T. ;

Zhou, J. ;

Sander, J. ;

Siddiqui, A. S. ;

Jones, S. J. M. .

NUCLEIC ACIDS RESEARCH, 2006, 34 :D68-D73

[6] Human-mouse alignments with BLASTZ [J].

Schwartz, S ;

Kent, WJ ;

Smit, A ;

Zhang, Z ;

Baertsch, R ;

Hardison, RC ;

Haussler, D ;

Miller, W .

GENOME RESEARCH, 2003, 13 (01) :103-107

[7] Gap statistics for whole genome shotgun DNA sequencing projects [J].

Wendl, MC ;

Yang, SP .

BIOINFORMATICS, 2004, 20 (10) :1527-1534

← 1 →