Re: [MUMmer-help] Help on Mummer.

[Adam P. <ada...@ya...>]

Hello Faddy,
 The main alignment routine at the core of nucmer (mummer's local aligner) is a modified version of the usual smith-waterman algorithm. The code is in "sw_align.hh" and "sw_align.cc" and the calling function is named "alignTarget" and documented in the header file. It is probably not what you are looking for because it is neither a true local aligner or global aligner. Instead, it extends an alignment outward from an anchor point and terminates the alignment when the similarity falls below a certain threshold. You are free to use the code as you wish, but it is probably not what you are looking for.
 
 Best,
 Adam Phillippy

Saad Faddy <sf...@t2...> wrote: 
Dear Sir,

My name is Faddy Saad, I would like to ask for your help on Mummer.
I am building a genome comparative mapping tool called MAGIC (as a part of 
an academic project) and I would like to integrate some code from Mummer 
and I do have some questions regarding the best way of doing so.

1. I am interested in performing pairwise local alignment on pairs
    of sequences and in order to do so I would like to call on a function
    from Mummer's source code directly from my c++ code.
    In order to reduce the time complexity, I don't want to use files,
    instead I would like to provide the alignment function two input char
    arrays (holding both sequences) and one output structure where the
    result will be held in.
    Is it possible to do that with Mummer?

2. Does Mummer include a pairwise global alignment method?
    Does it work on sequences of 200K length and more in a reasonable time?
    Is it possible to perform global alignment in the same way mentioned
    in ques 1 ?

I'd really appreciate your help.

With respect,
Faddy Saad.



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