Tag Archives: genotype

Tip of the Week: SwissVar, a New Genotype-phenotype Resource from SIB

SwissVar_tip_movieToday’s tip is on a new genotype/phenotype resource from the Swiss Institute of Bioinformatics, or SIB. I was already a fan of many SIB tools and resources, and was using one (ENZYME) when I found a notice about SwissVar. SwissVar is described as ‘a portal to Swiss-Prot diseases and variants.’ It includes information about genotype-phenotype relationships for each specific variant, manually annotated from literature. Manual annotation adds a level of quality and believability to this data. The SwissVar portal also contains various pre-computed information that may aid in determining the effect of the variant. Genotype-phenotype searches can begin with either Medical Subject Headings, or MeSH terms (Disease), gene or protein names (General characteristics) or variants (Functional/structural features). There are multiple ways to modify your searches, and results are clean tables of data including gene/protein accessions, names, links to MeSH definitions and links to variation reports.

If your research could benefit from high quality, manually curated genotype/phenotype information, I suggest you watch this tip, and then explore SwissVar according to your own interests.

SwissVar – a Portal to Swiss-Prot Diseases and Variants: http://www.expasy.ch/swissvar/

Tip of the Week: Phenotypic Data from the PhysioNet

PhysioNet TipOne of the things I’ve been thinking about lately are connections between genotype and phenotype – it is a topic in the news & I have been working on tutorials for the genotype-to-phenotype resources PhenomicDB & NCI’s dbGaP. Recently a friend notified of an article in Science featuring the PhysioNet – a resource intended to stimulate current research and new investigations in the study of complex biomedical and physiologic signals. The article was interesting & so I checked out this nice resource. In this short video I introduce you to a few of the features and data types available from the PhysioNet. You can read more about the PhysioNet, or see their mission statment by following the ‘continue reading’ link.

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A HuGE database

ResearchBlogging.org :) that was fun writing that title. A recent correspondence in Nature Genetics outlined some changes in the HuGE Navigator. This database has been available in some form since 2001. The basic purpose of the database is to…

navigate and mine the growing scientific literature on human gene-disease associations and related data in human genome epidemiology. As an interconnected system of applications that users can enter by using genes, diseases, or risk factors as the starting point, HuGE Navigator provides a potential bridge between epidemiologic and genetic research domains.

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A taste of OpenHelix

The bloggers here at OpenHelix and some of our family and friends decided to do the taste tests. You know the ones. You probably did them in your genetics class. I used them in my introductory biology class at CCSF years ago and had hundreds of the test strips left. So, we thought we’d distribute them to the bloggers and families here and see what the results were. The test strips are for sodium benzoate, PTC and thiourea. There is also a control strip of no taste (but paper). I numbered the strips and sent them to the bloggers and families (so they wouldn’t know what they were tasting, control or otherwise). And here are the results (and some database links to more about the genetics of taste):

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Tip of the Week: Visualizing Genotypes

SeattleSNPs genotypeAnd maybe it will help you visualize peace too :). There are several sites and software programs (Haploview and GVS are two) that will help you do visual genotype, we are going to show you one here that is simple to use at SeattleSNPs. This tip will show you how to access SeattleSNPs VG2 software and quickly visualize SNP allele genotype data for a gene, either your own data or that from the SeattleSNPs project.