PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes

被引：176

作者：

Conde, Lucia

Vaquerizas, Juan M.

Dopazo, Hernan

Arbiza, Leonardo

Reumers, Joke

Rousseau, Frederic

Schymkowitz, Joost

Dopazo, Joaquin ^{[1
]}

机构：

[1] Ctr Invest Principe Felipe, Dept Bioinformat, Valencia 46013, Spain

[2] Vrije Univ Brussel VIB, Switch Lab, B-1050 Brussels, Belgium

[3] CIPF Valencia, INB, Valencia 46013, Spain

来源：

NUCLEIC ACIDS RESEARCH | 2006年 / 34卷

关键词：

D O I：

10.1093/nar/gkl071

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 have developed a web tool, PupaSuite, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect, specifically oriented to help in the design of large-scale genotyping projects. PupaSuite uses a collection of data on SNPs from heterogeneous sources and a large number of pre-calculated predictions to offer a flexible and intuitive interface for selecting an optimal set of SNPs. It improves the functionality of PupaSNP and PupasView programs and implements new facilities such as the analysis of user's data to derive haplotypes with functional information. A new estimator of putative effect of polymorphisms has been included that uses evolutionary information. Also SNPeffect database predictions have been included. The PupaSuite web interface is accessible through http://pupasuite.bioinfo.cipf.es and through http://www.pupasnp.org.

引用

页码：W621 / W625

页数：5

共 31 条

[1] A haplotype map of the human genome [J].

Altshuler, D ;

Brooks, LD ;

Chakravarti, A ;

Collins, FS ;

Daly, MJ ;

Donnelly, P ;

Gibbs, RA ;

Belmont, JW ;

Boudreau, A ;

Leal, SM ;

Hardenbol, P ;

Pasternak, S ;

Wheeler, DA ;

Willis, TD ;

Yu, FL ;

Yang, HM ;

Zeng, CQ ;

Gao, Y ;

Hu, HR ;

Hu, WT ;

Li, CH ;

Lin, W ;

Liu, SQ ;

Pan, H ;

Tang, XL ;

Wang, J ;

Wang, W ;

Yu, J ;

Zhang, B ;

Zhang, QR ;

Zhao, HB ;

Zhao, H ;

Zhou, J ;

Gabriel, SB ;

Barry, R ;

Blumenstiel, B ;

Camargo, A ;

Defelice, M ;

Faggart, M ;

Goyette, M ;

Gupta, S ;

Moore, J ;

Nguyen, H ;

Onofrio, RC ;

Parkin, M ;

Roy, J ;

Stahl, E ;

Winchester, E ;

Ziaugra, L ;

Shen, Y .

NATURE, 2005, 437 (7063) :1299-1320

[2]

ARBIZA L, 2006, IN PRESS J MOL BIOL

[3] Beyond Mendel: An evolving view of human genetic disease transmission [J].

Badano, JL ;

Katsanis, N .

NATURE REVIEWS GENETICS, 2002, 3 (10) :779-789

[4] Haploview: analysis and visualization of LD and haplotype maps [J].

Barrett, JC ;

Fry, B ;

Maller, J ;

Daly, MJ .

BIOINFORMATICS, 2005, 21 (02) :263-265

[5] Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease [J].

Botstein, D ;

Risch, N .

NATURE GENETICS, 2003, 33 (Suppl 3) :228-237

[6] Listening to silence and understanding nonsense: Exonic mutations that affect splicing [J].

Cartegni, L ;

Chew, SL ;

Krainer, AR .

NATURE REVIEWS GENETICS, 2002, 3 (04) :285-298

[7] A vision for the future of genomics research [J].

Collins, FS ;

Green, ED ;

Guttmacher, AE ;

Guyer, MS .

NATURE, 2003, 422 (6934) :835-847

[8] PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes [J].

Conde, L ;

Vaquerizas, JM ;

Ferrer-Costa, C ;

de la Cruz, X ;

Orozco, M ;

Dopazo, J .

NUCLEIC ACIDS RESEARCH, 2005, 33 :W501-W505

[9] PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level [J].

Conde, L ;

Vaquerizas, JM ;

Santoyo, J ;

Al-Shahrour, F ;

Ruiz-Llorente, S ;

Robledo, M ;

Dopazo, J .

NUCLEIC ACIDS RESEARCH, 2004, 32 :W242-W248

[10] Efficiency and power in genetic association studies [J].

de Bakker, PIW ;

Yelensky, R ;

Pe'er, I ;

Gabriel, SB ;

Daly, MJ ;

Altshuler, D .

NATURE GENETICS, 2005, 37 (11) :1217-1223

← 1 2 3 4 →