SNP-VISTA: An interactive SNP visualization tool

BackgroundRecent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single Nucleotide Polymorphisms (SNPs) are established genetic markers that aid in the identification of loci affecting quantitative traits and/or disease in a wide variety of eukaryotic species. With today's technological capabilities, it has become possible to re-sequence a large set of appropriate candidate genes in individuals with a given disease in an attempt to identify causative mutations. In addition, SNPs have been used extensively in efforts to study the evolution of microbial populations, and the recent application of random shotgun sequencing to environmental samples enables more extensive SNP analysis of co-occurring and co-evolving microbial populations. The program is available at http://genome.lbl.gov/vista/snpvista[1].ResultsWe have developed and present two modifications of an interactive visualization tool, SNP-VISTA, to aid in the analyses of the following types of data: A. Large-scale re-sequence data of disease-related genes for discovery of associated and/or causative alleles (GeneSNP-VISTA). B. Massive amounts of ecogenomics data for studying homologous recombination in microbial populations (EcoSNP-VISTA). The main features and capabilities of SNP-VISTA are: 1) mapping of SNPs to gene structure; 2) classification of SNPs, based on their location in the gene, frequency of occurrence in samples and allele composition; 3) clustering, based on user-defined subsets of SNPs, highlighting haplotypes as well as recombinant sequences; 4) integration of protein evolutionary conservation visualization; and 5) display of automatically calculated recombination points that are user-editable.ConclusionThe main strength of SNP-VISTA is its graphical interface and use of visual representations, which support interactive exploration and hence better understanding of large-scale SNP data by the user.

[1]  E. Boerwinkle,et al.  DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene , 1998, Nature Genetics.

[2]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[3]  M. Daly,et al.  A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms , 2001, Nature.

[4]  D. Mccormick.  Sequence the Human Genome , 1986, Bio/Technology.

[5]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[6]  B. Spratt,et al.  Recruitment of a penicillin-binding protein gene from Neisseria flavescens during the emergence of penicillin resistance in Neisseria meningitidis. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Alberto Riva,et al.  SNPper: retrieval and analysis of human SNPs , 2002, Bioinform..

[8]  Jinghui Zhang,et al.  HapScope: a software system for automated and visual analysis of functionally annotated haplotypes. , 2002, Nucleic acids research.

[9]  M. Rieder,et al.  Sequence variation in the human angiotensin converting enzyme , 1999, Nature Genetics.

[10]  J. Banfield,et al.  Community structure and metabolism through reconstruction of microbial genomes from the environment , 2004, Nature.

[11]  P. Bork,et al.  Human non-synonymous SNPs: server and survey. , 2002, Nucleic acids research.

[12]  Aravinda Chakravarti,et al.  ViewGene: a graphical tool for polymorphism visualization and characterization. , 2002, Genome research.

[13]  Toshihiro Tanaka.  The International HapMap Project , 2003, Nature.

[14]  S. Tringe,et al.  Comparative Metagenomics of Microbial Communities , 2004, Science.

[15]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[16]  S. Henikoff,et al.  Accounting for human polymorphisms predicted to affect protein function. , 2002, Genome research.

[17]  Thomas Huber,et al.  Bellerophon: a program to detect chimeric sequences in multiple sequence alignments , 2004, Bioinform..

[18]  Hugues Sicotte,et al.  Genewindow: an interactive tool for visualization of genomic variation , 2005, Nature Genetics.