Tag Archives: gene function prediction

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: GeneMANIA for Fast Gene Function Predictions

I am happily the lucky scientist here at OpenHelix who has been selected to create a full tutorial on a network resource named GeneMANIA, but I just couldn’t wait to share some of the details about this resource’s great features. GeneMANIA stands for Multiple Association Network Integration Algorithm. Users can either input a single gene and see interaction networks associated with the gene, or (more powerfully) to enter a list of related genes and use GeneMANIA’s ‘state-of-the-art analysis algorithm’ to quickly and easily find additional related genes.

GeneMANIA allows a  scientist with no prior training in computational bioinformatics to easily use their gene list of interest to search a customized list of published functional genomics publications, as well as a wide variety of public databases, and receive the results of their analysis in an easy to interpret PDF report. Users can even upload their own important datasets and affect how the algorithm scores each gene and dataset. I  cannot cover all this functionality in this short tip – you’ll have to see our tutorial for that – but here I will show you how to do a basic search and some of the display features of GeneMANIA.

GeneMANIA stands for Multiple Association Network Integration Algorithm. For more information about it, please see this 2008 GeneMANIA publication, or the GeneMANIA documentation.