DigiPINS: a database for vertebrate exonic single nucleotide polymorphisms and its application to cancer association studies.
Single nucleotide polymorphisms (SNPs), which are the most abundant form of genetic variations in numerous organisms, have emerged as important tools for the study of complex genetic traits and deciphering of genome evolution. High-throughput genome sequencing projects worldwide provide an unprecedented opportunity for whole-genome SNP analysis in a variety of species. To facilitate SNP discovery in vertebrates, we have developed a web-based, user-friendly, and fully automated application, DigiPINS, for genome-wide identification of exonic SNPs from EST data. Currently, the database can be used to the mining of exonic SNPs in six complete genomes (Homo sapiens, Mus musculus, Rattus norvegicus, Canis familiaris, Gallus gallus and Danio rerio). In addition to providing information on sequence conservation, DigiPINS allows compilation of comprehensive sets of polymorphisms within cancer candidate genes or identification of novel cancer markers, making it potentially useful for cancer association studies. The DigiPINS server is available via the internet at http://pbil.univ-lyon1.fr/gem/DigiPINS/query_DigiPINS.php.
Navratil
Vincent
V
Laboratoire de Biométrie et Biologie Evolutive, Université Claude Bernard Lyon 1, 69622 Villeurbanne Cedex, France. navratil@biomserve.univ-lyon1.fr
Penel
Simon
S
Delmotte
Stéphane
S
Mouchiroud
Dominique
D
Gautier
Christian
C
Aouacheria
Abdel
A
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D015415:Biomarkers; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D016678:Genome; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D008969:Molecular Sequence Data; D009369:Neoplasms / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D012984:Software; D014584:User-Computer Interface
D015415:Biomarkers