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GPCR NaVa database

http://nava.liacs.nl/

Description :
The GPCR NaVa database describes sequence variants within the family of human G Protein-Coupled Receptors (GPCRs). GPCRs regulate many physiological functions and are the targets for most of today s medicines. The acronym NaVa stands for Natural Variant, which means any (non-artificial) variant that occurs in humans.
The GPCR NaVa database includes:
1) rare mutations (frequency below 1%);
2) polymorphisms (frequency above 1%), including Single Nucleotide Polymorphisms (SNPs);
3) variants without estimates of allele frequency.
The GPCR NaVa database aids GPCR research by categorising and integrating information on variants from databases and scientific papers. Moreover, the GPCR NaVa database is linked with the reputable GPCRDB.

Aknowledgement :
The GPCR NaVa database resulted from a joint project of the Leiden Medicinal Chemistry section of the Leiden/Amsterdam Center for Drug Research (LACDR) and the Leiden Institute of Advanced Computer Science (LIACS). We are very grateful to the Nederlandse organisatie voor Wetenschappelijk Onderzoek (NWO) for providing financial support.

References :
Kazius J., Wurdinger K., van Iterson M., Kok J., Back T., and Ijzerman A.P. (2008) GPCR NaVa database: natural variants in human G protein-coupled receptors. Hum Mutat. 29(1), 39-44.

ColiSNP

http://yayoi.kansai.jaea.go.jp/colisnp

Description :
Mapping non-synonymous SNPs on protein structures

FLYSNP

http://flysnp.imp.univie.ac.at/

Description :
SNP data for Drosophila melanogaster

SNP2NMD

http://variome.kobic.re.kr/SNP2NMD/

Description :
Human SNPs causing nonsense-mediated mRNA decay

F-SNP

http://compbio.cs.queensu.ca/F-SNP/

Description :
Functional effects of various human SNPs

HapMap Project

http://snp.cshl.org/

Description :
The SNP Consortium website (http://snp.cshl.org) has undergone many changes since its initial conception three years ago. The database back end has been changed from the venerable ACeDB to the more scalable MySQL engine. Users can access the data via gene or SNP keyword searches and browse or dump SNP data to textfiles. A graphical genome browsing interface shows SNPs mapped onto the genome assembly in the context of externally available gene predictions and other features. SNP allele frequency and genotype data are available via FTP-download and on individual SNP report web pages. SNP linkage maps are available for download and for browsing in a comparative map viewer. All software components of the DCC website (http://snp.cshl.org) are open source.

Recent develoments :
GMOD genome browser showing SNPs in context of genes and other features on the genome assembly. Gene keyword search. SNP allele frequency and genotype data, from a number of human populations (asian, african-american, african,caucasian).

References :
Sachidanandam, R., Weissman, D., Schmidt, S., Kakol, J., Stein, L., Marth, G., Sherry, S., Mullikin, J., Mortimore, B., Willey, D., Hunt, S., Cole, C., Coggill, P., Rice, C., Ning, Z., Rogers, J., Bentley, D., Kwok, P., Mardis, E., Yeh, R., Schultz, B., Cook, L., Davenport, R., Dante, M., Fulton, L., Hillier, L., Waterston, R., McPherson, J., Gilman, B., Schaffner, S., Van Etten, W., Reich, D., Higgins, J., Daly, M., Blumenstiel, B., Baldwin, J., Stange-Thomann, N., Zody, M., Linton, L., Lander, E., and Altshuler, D. ; The International SNP Map Working Group.(2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature, 409, 928-933.

SNPlogic

http://snplogic.org/

Description :
Interactive SNP annotation, selection and prioritization system for genotyping projects and/or analysis and interpretation of SNP data.

VarySysDB

http://h-invitational.jp/varygene/

Description :
Various types of human gene polymorphism

autoSNPdb

http://acpfg.imb.uq.edu.au/autosnpdb.php

Description :
Plant SNP discovery database

GenoWatch

http://genepipe.ngc.sinica.edu.tw/genowatch

Description :
A disease gene mining browser for association study. GenoWatch is a real-time batch SNP and short tandem repeat polymorphism pipeline that extracts current information from public domain websites such as NCBI, UniProt, KEGG and GO so that users can select the appropriate disease candidate genes.

PolySearch

http://wishart.biology.ualberta.ca/polysearch

Description :
PolySearch allows users to conduct comprehensive and associative queries, such as given X, find all Y's, where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also identifies, highlights and ranks abstracts, paragraphs or sentences.

Gramene

http://www.gramene.org/ Gramene is a curated, open-source, data resource for comparative genome analysis in the grasses. Our goal is to facilitate the study of cross-species homology relationships using information derived from public projects involved in genomic and EST sequencing, protein structure and function analysis, genetic and physical mapping, interpretation of biochemical pathways, gene and QTL localization and descriptions of phenotypic characters and mutations.

PolyPhred

http://droog.mbt.washington.edu/PolyPhred.html

Description :
UNIX-based tool for sequence trace based genotyping; integrated with Phred/Phrap/Consed (see DNA -- Contig Assembly); free for non-commercial use.

PolyDoms

http://polydoms.cchmc.org/polydoms/

Description :
PolyDoms is a database that maps human coding SNPs onto protein domains in an effort prioritize candidate mutations and polymorphisms.

PDA

http://pda.uab.es/pda2/

Description :
PDA (Pipeline Diversity Analysis) is a server which searches for polymorphic sequences in large databases, and estimates their genetic diversity. Results contain sequence alignments (generated by ClustalW) and include statistics on polymorphism, synonymous and non-synonymous substitutions, linkage disequilibrium, and codon bias for your alignment. The full results set is also available for download as a MySQL database.

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