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Web Services

Bovine SNP Annotation Tool (Snat) provides two functions to integrate various sources of biological information related to SNPs fast and conveniently, which is based on the built MySQL database working on the local webserver. With Snat, various sources of genomic information are integrated and retrieved from several leading online databases, including SNP information from dbSNP, gene information from Entrez Gene, protein features from UniProt/SWISS-PROT and UniProt/TrEMBL, linkage information from AnimalQTLdb, conserved elements from UCSC Genome Browser Database and gene functions from Gene Ontology, KEGG pathway and Online Mendelian Inheritance in Animals(OMIA).

The first function that is called "Search SNPs", helps you search bovine SNPs included in NCBI dbSNP and integrate related information from public domains such as dbSNP, Entrez Gene, UniProtKB, AnimalQTLdb, KEGG pathway, Gene Ontology, UCSC ConsElements and OMIA, when you specify a SNP coordinate like "Chr7,16345509", a SNP rs-identifier like "rs109234250", a region like "Chr14,410000-420000" or an index file containing lines of SNP coordinates or rs-identifiers. Many flexible options are provided to obtain a satisfactory result.
Click here or the top navigation bar to use the tool.

The second one that is called "Any Locus", helps you integrate related information of a single nucleotide no matter whether it is included in dbSNP. Also, various sources of genomic information from public domains are integrated and retrieved, including Entrez Gene, UniProtKB, AnimalQTLdb, KEGG pathway, Gene Ontology, UCSC ConsElements and OMIA.
Click here or the top navigation bar to use the tool.


Services For The Local Command Line

Besides the web service, Snat provides the service for the local command line.

The database of Snat is entirely copied into a SQL file, which is available for download. You can download it and import into the MySQL database in your own computer to build the database of Snat. Then you can download the two programmes and run in the command line of your own computer to perform annotation. The two locally running Perl programmes can be given many flexible options and offer the same functions as the web service of Snat.

Click here for details.

Note that this is very suitable for dealing with annotation for huge number of SNPs or loci.


Reference

Jiang J, Jiang L, Zhou B, Fu W, Liu JF, Zhang Q: Snat: a SNP annotation tool for bovine by integrating various sources of genomic information. BMC Genetics 2011, 12:85