new paper from my lab: IRiS

ResearchBlogging.orgThe latest paper published by people in my lab describes a method to reconstruct past Recombination Events:

  • MelĂ© M, Javed A, Pybus M, Calafell F, Parida L, Bertranpetit J, & The Genographic Consortium (2010). A New Method to Reconstruct Recombination Events at a Genomic Scale. PLoS computational biology, 6 (11) PMID: 21124860.

Let’s say that you have a set of genotypes obtained from a human population, like the HapMap project, the HGDP samples or a custom dataset: with this algorithm you can predict some of the recombination events that occurred in recent times.

While the most common approaches to analyze genotype panels datasets focus on identifying footprints of positive selection, association of a SNP with a disease, etc.. there have been few efforts to look at the history of recombination events. However, an event of recombination can have the same importance as any other mutation event. By knowing when a recombination has occurred we can infer useful information on the function and the history of the region involved.

What I like very much about this article is the impressive work of validation they have done to demonstrate the validity of their software. I am a silly person when it comes to the matter that bioinformatics software should be tested properly: but this time they have probably spent more time in testing the algorithm than in developing it.

The first approach they have used has been to carry out a lot of simulations, using the software CoSi. They have simulated the ‘whole history of the human species’ thousands of times, and then applied the algorithm on the simulated data to see how it performed. Afterwards, they have also used data from a sperm typing panel, which is a good dataset to study recombination events in human.

Predicting recent events of recombination from genotype data. The authors did a tremendous work to demonstrate the validity of their software.

So, if you want to know about a good paper with good examples on how to test a computational tool, you can have a look at this paper.

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