nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms

被引：171

作者：

Bao, L ^{[1
]}

Zhou, M ^{[1
]}

Cui, Y ^{[1
]}

机构：

[1] Univ Tennessee, Ctr Hlth Sci, Ctr Genom & Bioinformat, Dept Mol Sci, Memphis, TN 38163 USA

来源：

NUCLEIC ACIDS RESEARCH | 2005年 / 33卷

关键词：

D O I：

10.1093/nar/gki372

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：

Nonsynonymous single nucleotide polymorphisms (nsSNPs) are prevalent in genomes and are closely associated with inherited diseases. To facilitate identifying disease-associated nsSNPs from a large number of neutral nsSNPs, it is important to develop computational tools to predict the nsSNP's phenotypic effect (disease-associated versus neutral). nsSNPAnalyzer, a web-based software developed for this purpose, extracts structural and evolutionary information from a query nsSNP and uses a machine learning method called Random Forest to predict the nsSNP's phenotypic effect. nsSNPAnalyzer server is available at http://snpanalyzer.utmem.edu/.

引用

页码：W480 / W482

页数：3

共 17 条

[1]

BAO L, 2005, BIOINFORMATICS, DOI DOI 10.1093/BIOINFORMSTICS/BTI365

[2] A METHOD TO IDENTIFY PROTEIN SEQUENCES THAT FOLD INTO A KNOWN 3-DIMENSIONAL STRUCTURE [J].

BOWIE, JU ;

LUTHY, R ;

EISENBERG, D .

SCIENCE, 1991, 253 (5016) :164-170

[3]

Breiman L., 2001, Random Forest. Technical Report

[4] The ASTRAL Compendium in 2004 [J].

Chandonia, JM ;

Hon, G ;

Walker, NS ;

Lo Conte, L ;

Koehl, P ;

Levitt, M ;

Brenner, SE .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D189-D192

[5] HGVbase:: a human sequence variation database emphasizing data quality and a broad spectrum of data sources [J].

Fredman, D ;

Siegfried, M ;

Yuan, YP ;

Bork, P ;

Lehväslaiho, H ;

Brookes, AJ .

NUCLEIC ACIDS RESEARCH, 2002, 30 (01) :387-391

[6] Knowledge-based protein secondary structure assignment [J].

Frishman, D ;

Argos, P .

PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1995, 23 (04) :566-579

[7] Prediction of clinical drug efficacy by classification of drug-induced genomic expression profiles in vitro [J].

Gunther, EC ;

Stone, DJ ;

Gerwien, RW ;

Bento, P ;

Heyes, MP .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (16) :9608-9613

[8] Genome-wide analysis of single-nucleotide polymorphisms in human expressed sequences [J].

Irizarry, K ;

Kustanovich, V ;

Li, C ;

Brown, N ;

Nelson, S ;

Wong, W ;

Lee, CJ .

NATURE GENETICS, 2000, 26 (02) :233-236

[9] SIFT: predicting amino acid changes that affect protein function [J].

Ng, PC ;

Henikoff, S .

NUCLEIC ACIDS RESEARCH, 2003, 31 (13) :3812-3814

[10] Predicting deleterious amino acid substitutions [J].

Ng, PC ;

Henikoff, S .

GENOME RESEARCH, 2001, 11 (05) :863-874

← 1 2 →