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Friday, May 24, 2013

genome sequencing..

Genome sequencing is famous and one hottest area of bioinformatics and i would like to share my thoughts  on it:

 why sequencing of genome?

each and every gene should be studied and the function of the gene, operons, the base pare composition  also should be known for the entire genome or the entire chromosome. the genome sequencing also be useful for personalized medicine also for curing the diseases also  by sequencing the genome. the first sequenced whole  genome was H. Influenza and the bacteriophage MS2 . early the genome sequencing was done by Maxam gilbert and sangers method, well it is very popular method but its a tedious method,as the time changes the science also improves and grows fast and so many sequencing technologies where growing. the recent one is the next generation sequencing method.


Sequencing Costs:
The human genome sequencing project took 7 -8 years to complete the work about $ 1 billion. Then after this they proceed to sequence the 2nd genome of human it took around 3 – 4 months of about $30 million - $40 million. Now a days it costs around $ 5,000 and around 3 to 4 months maximum 6 months

SOLID :
     The one method which we are interested is SOLID lets see about the method and how its done ,
Its introduced by the Life technologies it is one of the method and here, the sequencing is done by the DNA ligase and it leads to the formation of beads with the adapter  each beads contains the same copies of DNA and those base pairs are further used, and the each base are represented in 4 different colors. then will get so much of data then the first step is assembly of data. we first clean or remove the unwanted data(remove vector adaptor) and the sequencing give the so many short fragments of the overlaps called contigs and those contigs may be the size of 4-5kb in. then the scaffolds are formed and we can find the size of the scaffolds by using the BAC insertion size.  the assembly is done by using FASTX file and we can get the plot.

LIBRARY FORMATION IN SOLID:


These are the steps which so far learnt from my PI and am interested to work in this so am writing this blog to show how much i understood might be some mistakes will be there or am unable to express properly, remaining part of sequencing after learning i will write in the next blog soon....

lets c some steps in Linux which i learnt:

1. once u started to work with the Linux need to install the fastx tool.
2. download the software.
(might download in the zipped format)
3. Then tar it by giving the command tar-xjf then give the filename.
4.then give the path name where the software is downloaded, to know the path use the command pwd.
5.then start installing the file.
6.if u have get any errors like  PKG_CONFIG or GTEXTUTILS  this path $ export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:$PKG_CONFIG_PATH
7. Then configure the path by giving ./ configure
8. type make
9. type make install
then the software is installed successfully then enjoy the sequencing.. happy sequencing...






7 comments:

  1. PI: dr. sucheta tripathy hope its not bad.....

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  2. I am really glad to see your post here and more so because you wrote without much of copy paste business. That is a significant feat, keep that up and post more articles...

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  3. PI Dr sucheta tripathy : thank u very much for the compliment and the more i learn from u the more i write here continuously mam...

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  4. wonderful Madhu. Looks like u understood very nicely.
    Keep It Up!!!!!!!!!!!

    ReplyDelete