Tag Archives: polymorphisms

Tip of the Week: F-SNP

fsnp_thumbThere are a lot of databases to search for to find SNP data, HapMap, dbSNP, SeattleSNPs, Genome Variation Server and many more. I’m going to add one more to your data mining arsenal, F-SNP. F-SNP (described more fully here in the 2008 NAR Database issue),

provides integrated information about the functional effects of SNPs obtained from 16 bioinformatics tools and databases. The functional effects are predicted and indicated at the splicing, transcriptional, translational, and post-translational level. As such, the F-SNP database helps identify and focus on SNPs with potential pathological effect to human health.

…as they say in the introduction. It looks to be a good first stop to find SNPs of functional relevance. The databases they pull from to get their information include several I’ve mentioned above and also the UCSC Genome database, Ensembl, SIFT and PolyPhen predictions and more. I’ve given a quick intro in the tip this week on how to get functional SNP information from F-SNP.

Tip of the Week: dbRIP

dbRIPthumb

Today’s tip of the week is introducing dbRIP, a database of Retrotransposon Insertion Polymorphisms in Humans. The dbRIP database, as you can tell from the title, is a focused resource on one subject: Retrotransposons in humans. Though focuses, retrotransposons are an important aspect of the human genome comprising 40% of it. They have an effect and a useful branch of study. This databases uses a local installation of the UCSC Genome Browser annotated with the RIP data. The tip movie (click the graphic to start) introduces you to the database. If it is something that interests you, you can learn more about how to use this database from the free UCSC Genome Browser tutorials at OpenHelix, since this database uses the same software.