CNVVdb: a Database of Copy Number Variations Across Vertebrate Genomes

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2009 Mar 27

PMID 19321736

Citations 3

Authors

Feng-Chi Chen

Yen-Zho Chen

Trees-Juen Chuang

Affiliations

Soon will be listed here.

Abstract

Summary: CNVVdb is a web interface for identification of putative copy number variations (CNVs) among 16 vertebrate species using the-same-species self-alignments and cross-species pairwise alignments. By querying genomic coordinates in the target species, all the potential paralogous/orthologous regions that overlap > or = 80-100% (adjustable) of the query sequences with user-specified sequence identity (> or = 60% ~ > or = 90%) are returned. Additional information is also given for the genes that are included in the returned regions, including gene description, alternatively spliced transcripts, gene ontology descriptions and other biologically important information. CNVVdb also provides information of pseudogenes and single nucleotide polymorphisms (SNPs) for the CNV-related genomic regions. Moreover, multiple sequence alignments of shared CNVs across species are also provided. With the combination of CNV, SNP, pseudogene and functional information, CNVVdb can be very useful for comparative and functional studies in vertebrates.

Availability: CNVVdb is freely accessible at (http://CNVVdb.genomics.sinica.edu.tw).

Citing Articles

A novel framework for the identification and analysis of duplicons between human and chimpanzee.

Chuang T, Wu S, Huang Y Biomed Res Int. 2013; 2013:264532.

PMID: 23984331 PMC: 3747353. DOI: 10.1155/2013/264532.

Online resources for genomic structural variation.

Sneddon T, Church D Methods Mol Biol. 2012; 838:273-89.

PMID: 22228017 PMC: 3804003. DOI: 10.1007/978-1-61779-507-7_13.

Gene family size conservation is a good indicator of evolutionary rates.

Chen F, Chen C, Li W, Chuang T Mol Biol Evol. 2010; 27(8):1750-8.

PMID: 20194423 PMC: 2908708. DOI: 10.1093/molbev/msq055.

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