Hardy-Weinberg

Hardy, Weinberg and Language Impediments
http://www.genetics.org/cgi/content/full/152/3/821

PrP allele (haplotype) and genotye frequencies in sheep II

I wrote about better display of PrP haplotype and genotype frequencies in last post. I have proposed a set of histograms instead of a table. However, parallel plot (R example 1, R example 2, random web article) is even better. Here is my attempt to use it on data compiled by Lühken et al. (2008):

• parallel plot of allele (haplotype) frequencies
• parallel plot of genotype frequencies

There is still room for improvement of the plot i.e. axis, ticks, ... For example, I would prefer to have 0-100 % scale on y axis. Anyway, the idea of parallel plot for haplotype/genotype frequencies in case of many haplotypes/genotypes should be clear. Here is also the data and R code to produce the plots.

PrP allele (haplotype) and genotye frequencies in sheep

Lühken et al. (2008) published estimates of PrP allele (haplotype) and genotye frequencies in for 56 sheep breeds in Europe and Middle East. They made a huge one-page table with all the numbers. Gosh, it is hard to read that table! There is to much info. It would be much better if they would plot this data. Well, I did and I think it is much more informative. I just copied their table into a spreadsheet and used R to do the plotting

• plot of allele (haplotype) frequencies
• plot of genotype frequencies

Browse Happy

http://browsehappy.com

Some hot animal science from Wageningen

Animal Science Group at Wageningen has a nice newsletter with hot news in animal science. Here is a list of link to newsletters:

• Newsletter 7
• Newsletter 6
• Newsletter 5
• Newsletter 4
• Newsletter 3
• Newsletter 2
• Newsletter 1
  

One more statistical package

I just came across another statistical package - aML.

Genetic diversity in human

There is a nice review paper "Going the distance: human population genetics in a clinal world" by Handley et al. They have a nice picture of earth globe with routes of colonization and genetic diversity. If you have access to Trends in genetics, these two links are very informative:

• globe picture
• relationship between genetic distance and distance
  

Lessons learned from the dog genome

Wayne and Ostrander wrote a paper "Lessons learned from the dog genome". Here is their abstract: "Extensive genetic resources and a high-quality genome sequence position the dog as an important model species for understanding genome evolution, population genetics and genes underlying complex phenotypic traits. Newly developed genomic resources have expanded our understanding of canine evolutionary history and dog origins. Domestication involved genetic contributions from multiple populations of gray wolves probably through backcrossing. More recently, the advent of controlled breeding practices has segregated genetic variability into distinct dog breeds that possess specific phenotypic traits. Consequently, genome-wide association and selective sweep scans now allow the discovery of genes underlying breed-specific characteristics. The dog is finally emerging as a novel resource for studying the genetic basis of complex traits, including behavior".

Progress in mapping sheep genome

http://www.engormix.com/e_news_view.asp?news=12256&AREA=OVI

LaTeX and Windows

Two pages (one static web page and blog post linking to the first) with LaTeX and Windows comparison:

• http://www.johndcook.com/blog/2008/04/03/microsoft-word-and-latex/
• http://www.ifs.hr/~mpinter/miktex.html

I think that blog spot is very relevant!