Introducing Qlixter

Comment, Chat and Blog on Every Website on the Internet!

The first technology to bring Social Networking features to every website online and the first to combine Social Networking and Search Engine technologies! Every search result…every website – Interactive!

Search “AltSearchEngines” and vote for us with a “thumbs up!”

Source: Qlixter

A number of tools for the examination of linkage disequilibrium (LD) patterns between nearby alleles exist, but none are available for quickly and easily investigating LD at longer ranges (>500kb). We have developed a web-based query tool (GLIDERS: Genome-wide LInkage DisEquilibrium Repository and Search engine) that enables the retrieval of pairwise associations with r2 [greater than or equal to] 0.3 across the human genome for any SNP genotyped within HapMap phase 2 and 3, regardless of distance between the markers.DescriptionGLIDERS is an easy to use web tool that only requires the user to enter rs numbers of SNPs they want to retrieve genome-wide LD for (both nearby and long-range).

The intuitive web interface handles both manual entry of SNP IDs as well as allowing users to upload files of SNP IDs. The user can limit the resulting inter SNP associations with easy to use menu options.

These include MAF limit (5-45%), distance limits between SNPs (minimum and maximum), r2 (0.3 to 1), HapMap population sample (CEU, YRI and JPT+CHB combined) and HapMap build/release. All resulting genome-wide inter-SNP associations are displayed on a single output page, which has a link to a downloadable tab delimited text file.

Conclusions: GLIDERS is a quick and easy way to retrieve genome-wide inter-SNP associations and to explore LD patterns for any number of SNPs of interest.

GLIDERS can be useful in identifying SNPs with long-range LD. This can highlight mis-mapping or other potential association signal localisation problems.

Author: Robert LawrenceAaron Day-WilliamsRichard MottJohn BroxholmeLon CardonEleftheria Zeggini
Credits/Source: BMC Bioinformatics 2009, 10:367

Source: 7th Space here