Finding QTLs with EXPLoRA

EXPLoRA is a Hidden Markov Model  (HMM) capable of finding Quantitative Trait Loci (QTL) using Bulk Segregant Analysis experiments.

A few days ago, our new version of the algorithm was made available thru a web server. You can find it following this link (here a link to the paper)

The idea behind the method is to use prediction of natural selection and linkage disequilibrium to detect the regions in the DNA responsible for the trait (i.e. find the QTL). Sexual reproduction involve two parents contributing one gamete each. Gametes are produced during meiosis: chromosomes are duplicated and then the cells are divided twice, ending in sexual cells with half the number of chromosomes of a normal cell. One key feature in this process is recombination or crossover.

Recombination is a fundamental source of genomic variation. It has a huge impact on the life cycle of mutations. Recombination cause the offspring to inherit a completely new combination of parental DNA. From the point of view of the dynamics of evolution this would allow a beneficial mutation to be selected independently of the rest of the ancestor’s mutations to some degree. This independence of mutations is not complete because the frequency of crossover events between two mutations is proportional to their physical distance in the chromosomes. Mutations close to each other are less likely to suffer a crossover event that separate them.

The degree to which mutations are separated is related to the recombination rate (i.e. the average number of recombination events that happen in a chromosome). The more recombination events in a chromosome, the easier it becomes for a beneficial mutation to be selected alone, just for the fitness advantage it confers. But this also implies that mutations in close vicinity tend to be inherited together, and therefore “linked”. The link between two mutations is known as linkage disequilibrium.

When observing the genomes of descendants that are selected for the traits of their parents, independent of the reason behind the selection the effect is that the causal mutation become more common in the population. Interestingly, this does not only happen to the responsible mutation, it also happen to those mutation in close proximity to the causal mutation. The closer a neutral mutation is to the causal mutation the less likely is that a recombination event happen in the area. If a neutral mutation is in very close proximity to the causal mutation, the chance that a recombination event happens in the region between them becomes very low.

Categories: Bioinformatics, QTL

Favorite Examples of Evolution

April 29, 2015 Leave a comment

Examples of evolution!

Telliamed Revisited

When the cold bites, When the review stings,When the news is sad, I simply remember these evolving things,And then I don’t feel so bad!— with apologies to Rodgers and Hammerstein

Over on Twitter, the biology students from George Jenkins High School in Lakeland, Florida, asked me and many others: “What’s your favorite example of evolution?”  There are so many fascinating examples that it’s hard for me to pick just one. So, here are half a dozen examples that are among my favorites.

  • The discovery by Neil Shubin and colleagues of Tiktaalik, an extinct fish (pictured below) from the Devonian that was poised to give rise to terrestrial vertebrates. You can read about this work in Shubin’s award-winning book, Your Inner Fish, which was also made into a PBS show.
  • The discovery by Svante Pääbo and colleagues of the Denisovans, an extinct lineage of…

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Categories: Uncategorized

Luria and Delbrück, 1943, Genetics

August 31, 2013 Leave a comment

R. Lenski talk about the fluctuation test (Luria/Delbrück experiment), very interesting!

Telliamed Revisited

Here’s the first of my blog posts on “must-read” papers.  I hope others will find these papers interesting and useful.

Luria, S. E., and Delbrück, M.  1943.  Mutations of bacteria from virus sensitivity to virus resistance.  Genetics28, 491–511.

[I’ve cobbled this post together by borrowing from a couple of previous writings where I explained why the Luria and Delbrück’s experiment is my all-time favorite.  One of these earlier pieces was a Q & A in Current Biology(2003); the other was an essay that appeared in Microbe (2011) and then in the book Microbes and Evolution: The World That Darwin Never Saw(2012).  I’ve also tweaked the text and added some bits to make things flow.]

Short summary:  An elegant experiment — sometimes called the “fluctuation test” — by Salvador Luria and Max Delbrück showed that new mutations that made bacteria resistant to phage (viruses that…

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Categories: Uncategorized

January 14, 2013 Leave a comment

Some people say that epigenetics are going to change completly the field of evolutionary biology. I think those are overreactions to cool words and reality will be that “findings in that area will also fit comfortably within modern evolutionary theory.”

Why Evolution Is True

The word “epigenetics” once meant simply “development”—that is, the way the genome worked itself into an organism through the production and regulation of proteins and absorption of food and materials from the outside, and the turning of some genes on and others off in different tissues.  Now, however, the term means roughly “forms of inheritance that rest on modification of the DNA sequence,” and by “DNA sequence” I mean the sequence of four bases (A, G, C, and T) that constitutes the DNA code.

We now realize, though, that some DNA bases can be modified, and in an inherited way, in a manner that can affect the development, behavior, or structure of an organism. Such modification often takes place via DNA methylation, in which some of those four bases acquire methyl groups, thereby changing how the DNA functions.

Such methylation, as you’ll see by reading the Wikipedia link above…

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Categories: Uncategorized

Open Acess books

September 6, 2011 Leave a comment

As a software developer the most amazing thing are Open Source projects, they are just awesome, they are free and they work perfectly, projects like apache are just one of the great things about Open Source.

In academia/research there are also some “Open” stuff, we have Open Access. For example, I am in love with Plos one and InTech, Plos one is an Open Access peer review journal and InTech publish Open Access books.

Do you know of any other Open Access resources? I would love to check them out.

Categories: Uncategorized

Finishing Linux installation

August 12, 2011 Leave a comment

I was trying to install linux and it is done 🙂

The guide proposed was a little outdated and not everything worked as smooth as possible but the information there was of big help. (Madman, thx again, great work)

To explain a little, the main problem was setting the NVidia video card in the Alienware M14X  to, actually, work; after my first installation try the problem was I could not see anything because the NVidia card did not worked; to fix this the procedure I followed was:

  • Install linux (ubuntu) with the power cord unpluged (so the NVidia card is not used)
Just download Ubuntu and create a bootable CD and follow a normal installation
  • Update the ubuntu kernel
The installation will leave your computer with kernel 2.6.38, we need to update it to the last version of the 2.6.39  available, at that moment was v2.6.39.4-oneiric (look at the mainline of kernels)
In the kernel page download the 3 files you need:
Go to wherever folder you downloaded them and run:
sudo dpkg -i <linux-headers all file> <linux-headers generic file> <linux-image file>
  • Install Bumblebee
sudo apt-add-repository ppa:mj-casalogic/bumblebee
sudo apt-get update
sudo apt-get install bumblebee

Configuring bumblebee select “Mario Höllein” or “MadmanMT” profile configuration

  • Configure the USB
Go to: /lib/modules/2.6.39-<versionyouinstalled>-generic/kernel/drivers/usb/storage$
Modify the name of all the *.ko files except usb-storage.ko
And have fun with linux 🙂
I will try to write about the installation of some bioinformatic packages
Categories: General

New Discovery channel series – Curiosity – great!

August 9, 2011 2 comments

I just saw the first episode of Curiosity: Did God create the universe?, very nice episode. I love to see scientist saying things that are uncomfortable and outside of the box, people have relegated science to just explain things outside of religion, but this is a nice example how science can answer big questions and that we will have to adapt our beliefs with reality.

I recommend to watch it to everybody, its an amazing show

Part 1, part 2, part 3 and part 4

The episode does gives a simple answer to the question it ask, Did God create the universe? Well… simply, No.

(I also recommend watch the discussion after the show, scientists and scholars giving opinions about that answer: Panel part 1, part 2)

Categories: General