[BiO BB] A series of Pairwise alignments

Ann Loraine aloraine at gmail.com
Sat Jun 3 10:00:23 EDT 2006


Probably you would want to run a pairwise alignment program over each
pair of seqs and then write some wrapper code around that to process
the data as you like.

The alignment program you select should be something that fits your
goal - do you want global or local alignment? What kind of scoring
system do you need? And so on.

For fun, take a look at:



On 6/3/06, hamid <hamid at ibb.ut.ac.ir> wrote:
>   Hi buddy,
>  Does anybody know how can I perform a series of pairwise alignments among
> all members of a set of proteins (almost 150 proteins) those I have their
> FastA sequences and sort mostly matched couples? I do not want to use
> ClustalW multiple alignment.
>  Yours,
>  Hamid
> /*
>  Hamid Nikbakht,
>  M.Sc of Cell and Molecular Biology,
>  Laboratory of Biophysics and Molecular Biology,
>  Bioinformatics Center,
>  Institute of Biochemistry and Biophysics(IBB),
>  University of Tehran,
>  Tehran,Iran.
>  Tel: +98-21-6111-3322
>  Fax: +98-21-6640-4680
>  Alt. E-mail: nikbakht at ibb.ut.ac.ir
> */
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Ann Loraine
Assistant Professor
Section on Statistical Genetics
University of Alabama at Birmingham

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