Sunday, January 27, 2013

Second Ramalingaswamy Conclave - In god's own country

I am currently sitting at the Thiruvananthapuram airport (being dropped by the hotel carpool system much earlier than the flight departure), have really got no other option other than writing something that is very recent. Sorry folks, this is not science, but soon we will separate this musing section from science in case you are just looking for science in this blog site. Just hang on till then...

Well, it goes this way: we all Ramalingaswamy fellows landed here in the early hours of 20th Jan 2013 in Thiruvananthapuram airport, got picked up to a transit. Sat on the lobby of this nice hotel for a couple of hours and then bundled up together to a nice scenic place called Kollam that has one of the nicest hotels - The Raviz. I can't rave enough about this hotel. The moment we checked in, tall saree clad young girls put tilak on our foreheads and handed over some delicious herbal drink. Then they led us to our rooms. The rooms were panoramic. Then we assembled at a place where lunch was arranged and the welcome ceremony began. I could not contain my happiness when I was told that our contingency amount was raised to 10 lakhs for the first year. I had this concern about hiring people from my contingency. In any case, that was the best news ever for me! People were amazingly friendly, food was super delicious. The meeting was very well organized by Rajiv Gandhi Center for Biotechnology. I must congratulate Dr. Meenakshi Munshi for doing such a wonderful job in taking care of all the administrative issues in a timely manner. She had the toughest jobs of interfacing between the govt. and the fellows and yet defending both parties when the opposite party questions certain things. I applaud her. So, also the entire mentor team including several amazing scientists such as Dr. Kanury Rao (ICGEB), Dr. Shubha Tole(TIFR), Dr. Usha Vijayaraghavan (IISc.), just to name a few. This led me to think that I have indeed taken the right decision to come back to India.

The presentations began from 21st onwards. It was truely inspiring to see all the scientists in their third years on the fellowship publishing 4-5 papers most of them in good impact factor journals about an average of 5 impact points. Few of the scientists were really amazing that have brought about paradigm shift in scientific belief systems working here in India. I personally benefited lot since I met with a person who is good at metabolic engineering and another person who has the neem genome assembly and another collaborator with whom I plan to work in near future.Overall, even if I spent 10 days away from my lab, I feel the time spent was really good.

On 25th I met Doctors, researchers, pharma company heads and my collaborator Dr. Susanta RoyChoudhury in Mumbai hospital about marker development and commercialization. It was truly an uplifting experience.

Tuesday, January 15, 2013

How to assign a name to an ip adress/redirect an ip adress

[Non-edited version] By Subhadeep Das
It often happens after creating a webserver, that, you have to type the ip iddress in the place reserved for URL in a web browser. It is cumbersome and appears very much annoying to people like us who are familiar using a domain name for a web server instead of ip. This can be resolved by adding the ip to a DNS server but in order to do that we need to send request to DNA administrator. The alternative and easiest way to solve the problem is to modify the "hosts" file of the Operating System of the local machine.

The "hosts" file can be found at computer/local Disk C/windows/System32/drivers/hosts (I don't know where it is located in linux  :(, sorry friends!!!  )

just add the line ip_address blank(or tab) desired_name_to_replace ip.

and you are done. from next time onwrds you just type instead of and the same webpage will be open.

But, wait friends, the step to edit the hosts file is not that easy. You won't be able to edit web file if you do not access the hosts file as Administrator.

To do it, follow the steps-

1)go to start menu
2)expand all programs
3)go to accessories
4)type notepad at search
5)right click on notepad
6)click on "Run as Administrator"
7)a blank notepad will be open, now go to file of notepad window
8)go to open
9)follow the path to hosts file, i.e go to local Disk C/windows/System32/drivers/hosts 
10)click open
11) add
12) save the file
13) enjoy.

Do it. You owe me a treat friends.   :D

Sunday, January 13, 2013

Multiparanoid, Inparanoid, inparalogs, outparalogs, orthologs

 Post genomics era, we have been flooded with large amount of genome wide information. Many taxonomic relationships between organisms are undergoing revision after their genome sequences were revealed. Studying core orthologous genes in a particular group of organism can shed light in understanding evolution and many pathogenic traits. Programs such as multiparanoid has been very useful in studying the orthologous relationship between organism. I will try to explain the program and the output in this blog.

This is a much confusing subject. Recently, I was asked a question by one of my students that led me into  putting things up here for public consumption. Post genomics era many new terms have been coined based on sequence similarity/divergence. We already know that genes undergo duplication in any given genome. They sometimes stay as a duplicate gene and sometimes mutate into an isoform or sometimes completely change themselves to code for an entirely different protein product. As long as they stay in the same genome, we call them paralogs. So, is there a difference between paralogs and alleles? Yes, there are. By classical genetic definition alleles exist at the same chromosomal location while paralogs exist in tandem.

Orthologs on the other hand stand for a gene in two different organisms that codes for more or less the same protein product and would have retained its identity through speciation. Now what are in-paralogs and out-paralogs? This is an event that involves both gene duplication and speciation. Lets say there is a gene A that undergoes duplication to A' in the same species. Now speciation took place giving rise to species X and species Y, both having gene XA, XA' and YA and YA'. Now we know XA -YA and XA' - YA' are orthologs to each other. What is the relationship between XA - XA' and YA - YA'? They are in-paralogs. Similarly XA - YA' and XA' - YA are out-paralogs. Diagrammatically, this can be represented as:

Figure 1.

[Taken from Inparanoid paper]

By definition outparalogs have undergone duplication before speciation, so they are not orthologs!

We are presently working on finding core orthogs in a certain sets of genomes belonging to one group. When we taxonomically classify organisms to a group, we do so based on morphological and behavioral patterns. But now we have the luxury to look at the genes. So, in order to get to the holi grail of core sets of proteins in Oomycetes organisms, we used Inparanoid and multiparanoid. Between a particular species pair (A and B), inparanoid runs 4 blastp searches:  A-B, B-A, A-A and B-B. It checks for outparalogs and keeps them away.
Multiparanoid on the other hand takes N * (N-1)/2 number of species comparison outputs from inparanoid and undertakes seed clustering till it merges all the inputs. Multiparanoid extends overlapping paired orthologous groups from Inparanoid, so in a given time, an error may get propagated. That is why Inparanoid needs to be run with stringent parameters (Default is also fine). It is also important to note that multiparanoid is designed to cluster species that originated near about the same time. If species that are diverged at different time scale used for clustering using multiparanoid, then you may not get the desirable outcome.