Tag Archives: mutation

SNPpets_2

Friday SNPpets

This week’s SNPpets illustrate that everyone’s back in the saddle after the holidays with plenty of chatter. New and updated databases, tools, and other news abound. The financial threat to well known databases like FlyBase, MGI, OMIM, Reactome, UniProt, etc–took my breath away though. Loved the RStudio cheat sheet. And the ProteinPaint lollipop plots of mutations looks great.


SNPpets_2Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…


https://twitter.com/sciencemagazine/status/682955226698100737

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Bad hair day, and a deviant search in the basement

badhair_mouse.jpgI have talked about how much I like the Mouse Genome mailing list before. It has high quality discussion, good job postings, handy meeting announcements, software discussions, and more. But today I LOLed at one of the best comments I have ever seen there (by Leigh Brian, of Duke):

I can’t believe you would list a mouse called “bad hair day” and NOT show a picture on the web site!

This was in response to a recent announcement about new mouse mutants that are available in a prior email:

Dear Readers,
Five new mouse models have been added to the MMR web site (http://mousemutant.jax.org/index.html). By clicking on the mutation symbol under the New Gene Mutations heading you will find descriptions for:

  • longjohn 3 Jackson (lgj-3J) a skeleton/limbs mutation on Chromosome 15.
  • Bad hair day (Bhrd) a new skin and hair mutation on Chromosome X.
  • Dreher 10 Jackson (dr-10J) a circling/hearing loss/ head toss mutation on Chromosome 1.
  • Dreher 11 Jackson (dr-11J) a circling/hearing loss/ head toss mutation on Chromosome 1.
  • small swaying lethal a new neurological mutation on Chromosome 6.

Notification of future new mutations and remutations added to the MMR website will be made via the mgi-list.

When I was at Jax as a post-doc one of the funniest announcements I ever heard in the workplace would come across the loudspeakers once a week: There will be a deviant search in the basement at 2 o’clock. There will be a deviant search in the basement at 2 o’clock. Swear to [deity]. At this point all the post-docs (except me) would run down to look at the odd mice that the caretakers observed that week. You could make your whole career with a compelling deviant mouse!! Grants, papers, tenure…those were some deviants. But I was in bioinformatics. All my deviants were code bugs.

Can you imagine–a career made from Bad hair day? That would be something. Almost makes me want to go back to the bench. Or back to MGI.

Tip of the week: SNPs on Protein Structure

The wealth of SNP data we are seeing these days is providing major insights into inheritance, population frequencies, effects on regulatory regions, splice sites and–of course–coding regions. Coding non-synonymous SNPs change the amino acid sequence of a protein. To get a sense of what that means on the protein structure you could use the GeneSNPs resource. We have a complete tutorial on GeneSNPs that you could watch. But to get a taste of how this data can be presented I’m going to show you a quick example of a SNP that changes an amino acid sequence on a protein structure. This is done with the PDBViewer tools at GeneSNPs. It requires MDL® Chime software for your browser. It is great to visualize the changes and think about what happens on your proteins of interest.

10x life?

Organism Lives 10 Times as Long After Genetic Tinkering

Longo and his team previously found two genes — RAS2 and SCH9 — related to growth and development of cancer that are similar in humans and yeast. They are so alike, in fact, that Longo said, “you can put the human gene in yeast and it works.”

So there are some antique yeasts out there. Really antique. And the researcher is Dr. Longo? How very fitting.

I’m intrigued about the mutations in the Ecuadoran population related to these genes. Looking forward to seeing this paper when it comes out in PLoS Genetics. We have been thinking about highly-conserved genes here lately and may “brew” a project on that, to show how various tools could be used to approach our questions. Continue reading