MutDB: update on development of tools for the biochemical analysis of genetic variation

被引：28

作者：

Singh, Arti ^{[1
]}

Olowoyeye, Adebayo ^{[1
]}

Baenziger, Peter H. ^{[1
]}

Dantzer, Jessica ^{[1
]}

Kann, Maricel G. ^{[2
]}

Radivojac, Predrag ^{[3
]}

Heiland, Randy ^{[4
]}

Mooney, Sean D. ^{[1
]}

机构：

[1] Indiana Univ, Sch Med, Dept Med & Mol Genet, Ctr Computat Biol & Bioinformat, Indianapolis, IN 46202 USA

[2] Univ Maryland Baltimore Cty, Dept Biol Sci, Baltimore, MD 21250 USA

[3] Indiana Univ, Sch Informat, Bloomington, IN 47406 USA

[4] Indiana Univ, Pervas Technol Labs, Indianapolis, IN 46202 USA

来源：

NUCLEIC ACIDS RESEARCH | 2008年 / 36卷

关键词：

D O I：

10.1093/nar/gkm659

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：

Understanding how genetic variation affects the molecular function of gene products is an emergent area of bioinformatic research. Here, we present updates to MutDB (http://www.mutdb.org), a tool aiming to aid bioinformatic studies by integrating publicly available databases of human genetic variation with molecular features and clinical phenotype data. MutDB, first developed in 2002, integrates annotated SNPs in dbSNP and amino acid substitutions in Swiss-Prot with protein structural information, links to scores that predict functional disruption and other useful annotations. Though these functional annotations are mainly focused on nonsynonymous SNPs, some information on other SNP types included in dbSNP is also provided. Additionally, we have developed a new functionality that facilitates KEGG pathway visualization of genes containing SNPs and a SNP query tool for visualizing and exporting sets of SNPs that share selected features based on certain filters.

引用

页码：D815 / D819

页数：5

共 31 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

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

Barrett, JC ;

Fry, B ;

Maller, J ;

Daly, MJ .

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

[3] The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 [J].

Boeckmann, B ;

Bairoch, A ;

Apweiler, R ;

Blatter, MC ;

Estreicher, A ;

Gasteiger, E ;

Martin, MJ ;

Michoud, K ;

O'Donovan, C ;

Phan, I ;

Pilbout, S ;

Schneider, M .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :365-370

[4] Mapping SNPs to protein sequence and structure data [J].

Cavallo, A ;

Martin, ACR .

BIOINFORMATICS, 2005, 21 (08) :1443-1450

[5] Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: Structure-based assessment of amino acid variation [J].

Chasman, D ;

Adams, RM .

JOURNAL OF MOLECULAR BIOLOGY, 2001, 307 (02) :683-706

[6] MutDB services: interactive structural analysis of mutation data [J].

Dantzer, J ;

Moad, C ;

Heiland, R ;

Mooney, S .

NUCLEIC ACIDS RESEARCH, 2005, 33 :W311-W314

[7]

Deshpande N, 2005, NUCLEIC ACIDS RES, V33, pD233

[8] Predicting deleterious nsSNPs: an analysis of sequence and structural attributes [J].

Dobson, Richard J. ;

Munroe, Patricia B. ;

Caulfield, Mark J. ;

Saqi, Mansoor A. S. .

BMC BIOINFORMATICS, 2006, 7 (1)

[9] PMUT:: a web-based tool for the annotation of pathological mutations on proteins [J].

Ferrer-Costa, C ;

Gelpí, JL ;

Zamakola, L ;

Parraga, I ;

de la Cruz, X ;

Orozco, M .

BIOINFORMATICS, 2005, 21 (14) :3176-3178

[10] A second generation human haplotype map of over 3.1 million SNPs [J].

Frazer, Kelly A. ;

Ballinger, Dennis G. ;

Cox, David R. ;

Hinds, David A. ;

Stuve, Laura L. ;

Gibbs, Richard A. ;

Belmont, John W. ;

Boudreau, Andrew ;

Hardenbol, Paul ;

Leal, Suzanne M. ;

Pasternak, Shiran ;

Wheeler, David A. ;

Willis, Thomas D. ;

Yu, Fuli ;

Yang, Huanming ;

Zeng, Changqing ;

Gao, Yang ;

Hu, Haoran ;

Hu, Weitao ;

Li, Chaohua ;

Lin, Wei ;

Liu, Siqi ;

Pan, Hao ;

Tang, Xiaoli ;

Wang, Jian ;

Wang, Wei ;

Yu, Jun ;

Zhang, Bo ;

Zhang, Qingrun ;

Zhao, Hongbin ;

Zhao, Hui ;

Zhou, Jun ;

Gabriel, Stacey B. ;

Barry, Rachel ;

Blumenstiel, Brendan ;

Camargo, Amy ;

Defelice, Matthew ;

Faggart, Maura ;

Goyette, Mary ;

Gupta, Supriya ;

Moore, Jamie ;

Nguyen, Huy ;

Onofrio, Robert C. ;

Parkin, Melissa ;

Roy, Jessica ;

Stahl, Erich ;

Winchester, Ellen ;

Ziaugra, Liuda ;

Altshuler, David ;

Shen, Yan .

NATURE, 2007, 449 (7164) :851-U3

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