PC sequence alignment program

Keith James kdj at fes6.sanger.ac.uk
Thu Feb 25 10:21:43 EST 1999


>>>>> "Francois" == Francois Jeanmougin <pingouin at crystal.u-strasbg.fr> writes:

    Francois> In article <sc4d82yhdl3.fsf at fes6.sanger.ac.uk>, Keith
    Francois> James <kdj at fes6.sanger.ac.uk> writes:
    >> If you want low cost/free for small numbers of sequences try
    >> Chromas to view ABI traces
    >> (http://www.technelysium.com.au/chromas.html) and then ClustalX
    >> for multiple alignments. You may find that ClustalX reads ABI
    >> directly, but I've a feeling it doesn't.

    Francois> 	It doesn't. Also it is designed to align
    Francois> phylogenetically realted sequence and not to build a
    Francois> sequencing project. Clustal is really not the solution
    Francois> to build sequence contigs.

I think I phrased my reply badly. I didn't intend to suggest that
Clustal be used for assembly! I assumed that the original poster had a
reason aligning DNA (and not translating it first) e.g. sequencing a
region of the same gene from many mutants with the same primer and
wanting a representation of the different base changes observed. There
are so many features in ClustalX these days that I would not have been
surprised if it could do something unusual like that.

-- 

Keith James  --  kdj at sanger.ac.uk  --  http://www.sanger.ac.uk/Users/kdj
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA




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