Tag Archives: amino acid

Tip of the Week: SIFT, Sorting (SNPs) Intolerant From Tolerant

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 interface, but is also used in various other tools to give indication of an amino acid substitution affect on  protein function. If you want to learn more about how the predictions are made (and some comparisons of the different methodologies), you might want to check out their paper (warning, pdf file).

Tip of the Week: Amino acid sequences in the UCSC Genome Browser

People are using the UCSC Genome Browser to visualize and analyze many important genomic features. During our training sessions we have found that people sometimes don’t realize how they can see the amino acid sequences in the browser. When you have zoomed into a region enough you can actually see a three-frame translation of the genomic sequence in the viewer.

Ah-ha, you say! But there should be six frames, right?

Watch this “tip of the week” to see how to display the other 3-frames.

To learn more about other aspects of visualizations in the Genome Browser you can see the full tutorial.