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Bioinformatics Advance Access originally published online on January 18, 2008
Bioinformatics 2008 24(7):1011-1013; doi:10.1093/bioinformatics/btn002
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

PGMapper: a web-based tool linking phenotype to genes

Qing Xiong 1,2, Yuhui Qiu 2 and Weikuan Gu 1,*

1Department of Orthopedic Surgery-Campbell Clinic, University of Tennessee Health Science Center, Memphis, TN 38163, USA and 2Department of Computer Science and Technology, Southwest University, Chongqing 400715, P.R. China

*To whom correspondence should be addressed.


  Abstract

Summary: With the availability of whole genome sequence in many species, linkage analysis, positional cloning and microarray are gradually becoming powerful tools for investigating the links between phenotype and genotype or genes. However, in these methods, causative genes underlying a quantitative trait locus, or a disease, are usually located within a large genomic region or a large set of genes. Examining the function of every gene is very time consuming and needs to retrieve and integrate the information from multiple databases or genome resources. PGMapper is a software tool for automatically matching phenotype to genes from a defined genome region or a group of given genes by combining the mapping information from the Ensembl database and gene function information from the OMIM and PubMed databases. PGMapper is currently available for candidate gene search of human, mouse, rat, zebrafish and 12 other species.

Availability: Available online at http://www.genediscovery.org/pgmapper/index.jsp

Contact: wgu{at}utmem.edu; qxiong1{at}utmem.edu

Associate Editor: Chris Stoeckert

Received on October 5, 2007; revised on November 19, 2007; accepted on January 1, 2008

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