Comparison of genome sequences

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Biolink
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Comparison of genome sequences

Well i got two genome sequences at hand, one is a prokaryotic genome and th other one is an eukaryotic genome sequence. Im asked to compare the genome sequence of both to find out the gene size, presence of microsatellites. Can anyone explain me ind etail how to go about with the comparison and i dont have basic knowledge in this. Kindly help me with detailed explanation pleaseeeeeeeeeeeee.

Biju
Biju's picture
Hi dollycaddu

Hi dollycaddu
You could start with Blast from NCBI site for the genome sequence comparisons. Another advanced level site you could use is UCSC genome browser. But I will start with Blast first.In the process you will learn additonal websites to look for and related information. Hoep this helps. Reply if you expereince any problems.
Biju Joseph

Biolink
Biolink's picture
Hello Biju,

Hello Biju,

First of all thanks a bunch for your prompt resposne. I did go through the Blast in NCBI website, while i was trying to browse thorugh i landed on a page where im asked to provide my genome sequence, well im having two sequences at hand. I got only one box, if i want to comapre both the sequence what should i do. There is one option in the page which says Allign two or more sequences, when i click on the option im getting two boxes to paste my genomes. When i paste my two separate sequences here, will i be getting comparative results. Apart form this how will i come to know the size of my genome and the presence of microsatellite. Could you eloborate over this pleaseeeeeee.

rajasereddy
rajasereddy's picture
Hi dollycaddu

Hi dollycaddu

This link could help you for sequence alignment.
http://www.ebi.ac.uk/Tools/sequence.html

For MicroSattelite of STR finding you should use some os the programs for that purpuse such as http://biophp.org/minitools/microsatellite_repeats_finder/demo.php

regars
reddy

Biju
Biju's picture
sorry fior the delayed

sorry fior the delayed ersponse. I think you should  be able to get the aligned sequcs if you paste both  sequecs in the 2 boxes.I will visit the site and let you more in detail.

Biju

Biolink
Biolink's picture
Thanks a lot Raj for your

Thanks a lot Raj for your interest. Biju thank you once again for your response. Thank you turning up again and awiating your detailed repsonse regarding the question.

ncwildb88
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Confused. I don't even know

Confused. I don't even know how to answer these practice problems my mentor gave me to help me learn deep sequencing ( I have never done anything in the genetics field before).
 One flow cell on the Illumina HiSeq 2000 produces 100 gigabases of output. Assuming uniform coverage across the genome and taking into account the contamination issues show how much depth of coverage per genome would you get from:

mso-bidi-font-family:Tahoma">(a)             a multiplexed sample containing 10 Dengue virus genomes, with 50% virus DNA

mso-bidi-font-family:Tahoma">(b)             a multiplexed sample containing 5 Herpes Simplex virus genomes with 90% virus DNA

mso-bidi-font-family:Tahoma">(c)             a single sample of Rickettsia rickettsii
italic"> with 100% bacterial DNA