Last tip I did was on PolyPhen, an algorithm that helps predict the phenotypic result of a non-synonymous SNP. There are other such algorithms available including MAPP (Multivariate Analaysis of Protein Polymorphism), SNPs3D and SIFT (Sorting Intolerant From Tolerant). It’s the latter that today’s tip will be briefly covering. SIFT, like PolyPhen, has a web [...]
There are several methods that can be used to predict if a particular non-synonymous SNP is deleterious; SIFT and PolyPhen, among others. Which one to use will be up to the individual researcher and the strengths and weakness of the predictors, though the two mentioned do a pretty good job. Today’s tip will be on the web [...]
About 6-7 months ago, Mary mentioned that R-Genetics analysis was coming to Galaxy. Well, it has now and is available at the public Galaxy site. The old Rgenetics site links to the new one and the information about using Galaxy as a wrap around interface for the Rgenetics project tools. Today’s tip just points you [...]
This next post in our continuing semi-regular Guest Post series is from Andrew Johnson, one of the developers and the concept designer of SNAP, SNP Annotation and Proxy Search which is hosted at the Broad Institute. If you are a provider of a free, publicly available genomics tool, database or resource and would like to convey [...]
The last tip of the week I did was Genome Variation Tour I where we started our journey following one SNP in an individual’s genome through various databases to see what we can find out about that variation. In that tip we started out by looking at a SNP in the CYP4F2 gene in the [...]
This next post in our continuing semi-regular Guest Post series is from Pedro Lopez, developer of WAVe at the University of Aveiro Bioinformatic Group in Aveiro Portugal. If you are a provider of a free, publicly available genomics tool, database or resource and would like to convey something to users on our guest post feature, [...]
Today’s Tip of the Week is a short introduction to WAVe, or the Web Analysis of the Variome. The tool was recently introduced to us, and I’ve found it a welcome introduction to the tools available to the researcher to analyze human variation. This is apropos considering the recent paper we’ve been discussing on the clinical [...]
HapMap has had a few minor updates to their browser, and importantly, new phase 3 data was released early last year (drafts of that data were released in 2008). Haploview, the downloaded software that allows the user to perform in depth LD and haplotype analysis, has been recently updated from version 4.1 to version 4.2. [...]
Interesting post from SNPedia blog (we mentioned being able to view SNPedia SNPS HapMap last year in a post) of the top 10 SNPs of the year. Of course, as they mention, it’s very subjective. Because they have chosen SNPs with serious health interest, I’ll semi-frivolously (because hey, no knowledge is necessarily “frivolous” nominate either: [...]
Perusing my copy of Nature Genetics last week, I was flipping through the pages and noticed an unusual graphic. I looked at it a little closer and was convinced it was one of the Spirographs that I used to make as a kid. (Remember those? I always liked that….) I looked a little bit closer [...]
Recent Comments