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Bioinformatics Advance Access originally published online on March 25, 2009
Bioinformatics 2009 25(11):1419-1421; doi:10.1093/bioinformatics/btp166
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© 2009 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.

CNVVdb: a database of copy number variations across vertebrate genomes

Feng-Chi Chen 1, Yen-Zho Chen 2 and Trees-Juen Chuang 2,*

1Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Miaoli County 350 and 2Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan

*To whom correspondence should be addressed.


  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 ≥80–100% (adjustable) of the query sequences with user-specified sequence identity (≥60%~≥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.

Contact: trees{at}gate.sinica.edu.tw

Associate Editor: Alfonso Valencia

Received on December 3, 2008; revised on March 2, 2009; accepted on March 17, 2009

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