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Old 05-30-2017, 10:01 AM   #1
jeevansai
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Post Comparing two genome sequences

I am learning how to compare two genome sequences to find how similar they are i did not find any resource related to it.

Now say if i want to compare them should i use local alignment or global alignment or any other modified algorithm and how do i give rating to them.

How will the match vary in case if i am comparing between two species for different dna sample.Can someone give any reference to the algorithm.Thank you.
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Old 05-30-2017, 10:14 AM   #2
Richard Finney
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Check out:
https://blast.ncbi.nlm.nih.gov/Blast..._LOC=align2seq

This used to be called "bl2seq". Just play around with it by supplying two similar sequences. This should be pretty straightforward; you can figure out the quality metrics.
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Old 05-30-2017, 10:32 AM   #3
jeevansai
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I saw the tool, i just want to learn the algorithm to know the way it is done could you please provide me some resource briefly explaining the method.Thank you.
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Old 05-30-2017, 11:15 AM   #4
GenoMax
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Fore reference crossposted: https://www.biostars.org/p/255297/
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Old 05-30-2017, 02:22 PM   #5
JohnN
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You could alway try mauve aligner: http://darlinglab.org/mauve/mauve.html
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Old 05-30-2017, 09:57 PM   #6
jeevansai
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But i want the clear method on how to do it as i want to code myself.
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