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.
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.
Mauve paper describes the methodology it uses.
There is no explanation about the algorithm,they just gave the link for their source code and that too not working.
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.
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
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Hello jeevansai502!
Cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=76279