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Bioinformatics. 2009 Jun 1;25(11):1419-21. doi: 10.1093/bioinformatics/btp166. Epub 2009 Mar 25.

CNVVdb: a database of copy number variations across vertebrate genomes.

Author information

  • 1Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Miaoli County 350, Taipei, Taiwan.

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).

PMID:
19321736
PMCID:
PMC2682513
DOI:
10.1093/bioinformatics/btp166
[PubMed - indexed for MEDLINE]
Free PMC Article
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