The last tip of the week I did was Genome Variation Tour I where we started our journey following one SNP in an individual’s genome through various databases to see what we can find out about that variation. In that tip we started out by looking at a SNP in the CYP4F2 gene in the [...]
Comprehensive tutorials on the publicly available NCBI resources enable researchers to quickly and effectively use these invaluable resources. Seattle, WA (PRWEB) June 8, 2010 – OpenHelix today announced the availability of three updated tutorials on NCBI resources. The National Center for Biotechnology Information, NCBI, is home to many of the most commonly used publicly available databases and [...]
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 [...]
The Lancet paper, Clinical assessment incorporating a personal genome, has held my fascination this weekend (yes, I read it at the beach). Mary posted Friday and again Saturday on the paper and related NPR segment. It feels to me to be a seminal paper, though I do agree with Daniel at Genetic Future, there are [...]
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 [...]
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, [...]
We go through the thousands of resources and databases available online in our search to do tutorials we found many that are great resources but for one or more reasons we don’t or can’t do a tutorial for. Yet they are great resources. So, we occasionally do “Tip of the Week” on some, but even [...]
Mary pointed out (and I’ve Tivo’d for my daughter, the great lover of rats) that the History channel had a special on rats recently. Well, not to be outdone, Nature Genetics May issue is all about rats. There are some great articles in that issue about rat genetics and rat genetics as a model for [...]
For funding reasons, NCBI (home of PubMed, BLAST, dbSNP, OMIM and more) has cut their outreach staff, canceled all onsite training seminars and this has to mean decreased support for online help, documentation and tutorials. When we wrote our NIH grant, one of the models of success in the bioinformatics training area that we highlighted [...]
A lot of researchers use dbSNP, some don’t know that you can blast the dbSNP database with a query sequence of interest to find out if there is a polymorphism reported for a homologous sequence in the database. You can, it’s simple, use Blast SNP. It’s not a prominent link, so you might of overlooked [...]
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