Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications

被引：60

作者：

Ondov, Brian D. ^{[1
]}

Varadarajan, Anjana ^{[1
]}

Passalacqua, Karla D. ^{[1
]}

Bergman, Nicholas H. ^{[1
,2
]}

机构：

[1] Georgia Inst Technol, Sch Biol, Atlanta, GA 30332 USA

[2] Georgia Tech Res Inst, Electroopt Syst Lab, Atlanta, GA 30332 USA

来源：

BIOINFORMATICS | 2008年 / 24卷 / 23期

关键词：

D O I：

10.1093/bioinformatics/btn512

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Here, we report the development of SOCS ( short oligonucleotide color space), a program designed for efficient and flexible mapping of Applied Biosystems SOLiD sequence data onto a reference genome. SOCS performs its mapping within the context of 'color space', and it maximizes usable data by allowing a user-specified number of mismatches. Sequence census functions facilitate a variety of functional genomics applications, including transcriptome mapping and pro. ling, as well as ChIP-Seq.

引用

页码：2776 / 2777

页数：2

共 8 条

[1] Genome-wide mapping of in vivo protein-DNA interactions [J].

Johnson, David S. ;

Mortazavi, Ali ;

Myers, Richard M. ;

Wold, Barbara .

SCIENCE, 2007, 316 (5830) :1497-1502

[2] EFFICIENT RANDOMIZED PATTERN-MATCHING ALGORITHMS [J].

KARP, RM ;

RABIN, MO .

IBM JOURNAL OF RESEARCH AND DEVELOPMENT, 1987, 31 (02) :249-260

[3] SOAP: short oligonucleotide alignment program [J].

Li, Ruiqiang ;

Li, Yingrui ;

Kristiansen, Karsten ;

Wang, Jun .

BIOINFORMATICS, 2008, 24 (05) :713-714

[4] The transcriptional landscape of the yeast genome defined by RNA sequencing [J].

Nagalakshmi, Ugrappa ;

Wang, Zhong ;

Waern, Karl ;

Shou, Chong ;

Raha, Debasish ;

Gerstein, Mark ;

Snyder, Michael .

SCIENCE, 2008, 320 (5881) :1344-1349

[5] Accurate multiplex polony sequencing of an evolved bacterial genome [J].

Shendure, J ;

Porreca, GJ ;

Reppas, NB ;

Lin, XX ;

McCutcheon, JP ;

Rosenbaum, AM ;

Wang, MD ;

Zhang, K ;

Mitra, RD ;

Church, GM .

SCIENCE, 2005, 309 (5741) :1728-1732

[6] Using quality scores and longer reads improves accuracy of Solexa read mapping [J].

Smith, Andrew D. ;

Xuan, Zhenyu ;

Zhang, Michael Q. .

BMC BIOINFORMATICS, 2008, 9 (1)

[7] Gene expression profiling by massively parallel sequencing [J].

Torres, Tatiana Teixeira ;

Metta, Muralidhar ;

Ottenwalder, Birgit ;

Schlotterer, Christian .

GENOME RESEARCH, 2008, 18 (01) :172-177

[8] Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution [J].

Wilhelm, Brian T. ;

Marguerat, Samuel ;

Watt, Stephen ;

Schubert, Falk ;

Wood, Valerie ;

Goodhead, Ian ;

Penkett, Christopher J. ;

Rogers, Jane ;

Bahler, Jurg .

NATURE, 2008, 453 (7199) :1239-U39

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