iDatamining.org

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Please contact with me at yiyu.jia@iDataMining.org!

Thursday, May 20, 2010

statistical analysis on Intron/Exon splice sites distribution


After the discovery of nuclear introns in 1970s, Harvard biologist Walter Gilbert, who coined both terms "intron" and "exon" in 1978, raised one more question: "Why are genes in pieces?". Meanwhile, he also hypothesized that eukaryotic genes had been assembled from mini-genes -- today's exons. Most eukaryotic genes have intron/exon structure. Whether the intron/exon structure of eukaryotic genes is the result of the shuffling of exons at an early evolutionary stage, or introns have been inserted into preformed genes during eukaryotic evolution at the late evolutionary stage is the core question of the ongoing debate between "introns-early" and "introns-late" camps. Neo-Darwinists prefer "introns-early" because this hypothesis allows modern genes to be composed from small pieces of "mini-gene". Nobel prize winner Renato Dulbecco says that introns could not have been inserted late, because there are too many similarities among the introns found in species that diverged very long ago. However, recent research work show that modern nuclear introns invaded eukaryotic genes late in evolution after the separation of transcription and translation.

I became to be interested in this research topic very much as it is even about the origin of genes (if we accept the hypothesis of evolution)! It is interesting that I feel research on this is built on hypothesis and hypothesis on hypothesis. However, what science research is eventually started from a hypothesis? It is science. It is very interesting that, as human being, we are so curious to find out origin of us! But, can it be a completion task for us? I really do not know. Therefore, as a conclusion of my research thesis, I find out a Chinese poems written by Su Shi around one thousand years ago. 

             Written on the Wall at West Forest Temple
                                                                 by Su Shi
                  From the side, a whole range; 

                  from the end, a single peak: 
                  Far,near, high, low, no two parts alike. 
                 Why can't I tell the true shape of Lu-shan? 
                 Because I myself am in the mountain.
                                                          Translated by Tr. Burton Watson
 

If you are interested, Click for my thesis about gene evolution  . Here are comments from reviewers (click here).  Here is my defense letter. You will have fun (click here and here). 

Monday, May 10, 2010

Configure auto login on Fedora 13 or Fedora 14

I was tired about typing password on my home notebook every time when I turn it on. Especially, I want to turn it on and leave for doing other things. Then, I do not need to waste time on waiting it to boot up. After doing searching online and trying, the below is the way to enable the auto login for GNOME. And, it is the same if I want enable KDE desktop auto login. It seems wired. But, I think it is reasonable because there is no reason to let KDE not auto login if the GNOME's auto login has been enabled.

To enable auto login in Fedora 13 is simple,
  1.  change account to be su 
  2. open file /etc/gdm/custom.conf in a text editor
  3. change or add below into the file
[daemon]
TimedLoginEnable=true
TimedLogin=yiyu.jia
TimedLoginDelay=0

This works on Fedora 14 as well.