Comparing two genome sequences

jeevansai · 05-30-2017, 11:01 AM

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.

Richard Finney · 05-30-2017, 11:14 AM

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.

jeevansai · 05-30-2017, 11:32 AM

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.

GenoMax · 05-30-2017, 12:15 PM

Fore reference crossposted: https://www.biostars.org/p/255297/

JohnN · 05-30-2017, 03:22 PM

You could alway try mauve aligner: http://darlinglab.org/mauve/mauve.html

jeevansai · 05-30-2017, 10:57 PM

But i want the clear method on how to do it as i want to code myself.

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05-30-2017, 11:01 AM	#1
jeevansai Junior Member Location: India Join Date: May 2017 Posts: 4	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.

05-30-2017, 11:14 AM	#2
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	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.

05-30-2017, 11:32 AM	#3
jeevansai Junior Member Location: India Join Date: May 2017 Posts: 4	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.

05-30-2017, 12:15 PM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Fore reference crossposted: https://www.biostars.org/p/255297/

05-30-2017, 03:22 PM	#5
JohnN Member Location: Toronto Join Date: Jan 2011 Posts: 30	You could alway try mauve aligner: http://darlinglab.org/mauve/mauve.html

05-30-2017, 10:57 PM	#6
jeevansai Junior Member Location: India Join Date: May 2017 Posts: 4	But i want the clear method on how to do it as i want to code myself.