Comparing two genome sequences

Question

[jeevansai502]

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.

[GenoMax]

Hello jeevansai502!

Cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=76279

Answer 1

[GenoMax]

Take a look at mauve (if you are looking for bacterial genomes). LASTZ is meant to align chromosome size pieces for larger genomes.

[jeevansai502]

It is a tool and the source code is very large 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]

Mauve paper describes the methodology it uses.

[jeevansai502]

There is no explanation about the algorithm,they just gave the link for their source code and that too not working.

[GenoMax]

Did you not see/read the Methods section in the paper linked above (excerpt below)?

The alignment algorithm can be summarized as follows:

    Find local alignments (multi-MUMs).

    Use the multi-MUMs to calculate a phylogenetic guide tree.

    Select a subset of the multi-MUMs to use as anchors—these anchors are partitioned into collinear groups called LCBs.

    Perform recursive anchoring to identify additional alignment anchors within and outside each LCB.

    Perform a progressive alignment of each LCB using the guide tree.

Aaron Darling moved to Australia and the link I provided in 1st post is for his current lab/mauve site.

[jeevansai502]

Now if i am comparing two human genomes then both will be of approximately same size range so how will i do local alignment there and how to do the algorithm on such huge genome

[GenoMax]

LASTZ, also linked above, is meant for that application. Locate the paper/Bob Harris' thesis and you will have the alogorithmic details.