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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 to the tool and gives you a quick overview of what is there. …

Today’s tip is the continuation of researching a single SNP in an individual genome. Trey will use a dbSNP RS ID to find linkage disequilibrium information between a SNP of interest and SNPs in the region easily and quickly. GVS , the Genome Variation Server at the University of Washington to analyze a dbSNP rs ID of your choice. This 3 minute screencast will show you how to …

Today’s tip of the week is actually the first in a series of tips I will be doing over the next couple months. The recent paper in Lancet did a clinical assessment of an individual genome. In doing so, the researchers used various genomic resources do ascertain and interpret the data . We have a free tutorial on NIEHS SNPs that walks through some of these resources, but I thought …

Ratmine is a ‘data warehouse’ that allows the user to construct queries across different areas of biological knowledge from SNPs to Pathways. It’s developed by the people at RGD and uses Intermine a project developed for Flymine and as part of a project between RGD , SGD and ZFIN to implement Intermine for these databases and ” develop new methods of …

As Trey posted last week in part I, we’ve been doing tips-of-the-week for two years now. We have completed over 100 little tidbit introductions to various resources*.  At the end of the year we are doing a summary post to collect them all.  If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

I’ve got the second half of …

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 and realized it was somewhat more informative than the Spirographs I used to draw.  This …

In an earlier What’s Your Problem thread , a researcher had hundreds of SNP locations where they were trying to easily obtain the flanking sequence of those hundreds of SNPs without having to go to each location in the UCSC Genome Browser and eyeballing. There are probably a few ways to do this, but I found that Galaxy was a good place to start. So, the tip this week is taking two …

There 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 …

dbSNP is the largest polymorphism database available, including SNPs from many different organisms. dbSNP now has a new search mechanism that allows the researcher to search using HGVS nomenclature for human variation. Not only this, but the feature allows you to annotate the dbSNP rs record that you found, or if you haven’t found one, add the new information to the database. To …

So, this week we will have finished a full year of our “Tips of the Week” series. Every Wednesday we post a short 3-5 minute movie of a tip on how to use a resource or database. We’ve done one year’s worth! So, for the end of this year, we are going to list them here for you. This week we’ll list the first 6 months worth of tips, next week we’ll go over the next 6 months.

Dec. …