Sequence alignment

Daniel Nilsson daniel.nilsson at genpat.uu.se
Tue Oct 24 07:51:35 EST 2000



> I am trying to align different sequences from the genebank. The best program
> I've found so far is BioEdit (Im using PC - Windows or Linux), which uses
> ClustalW to align sequences. I've managed to align two sequences (one of 930
> bp, theother of 2220 bp) with ClustalW, which has been aligned in an
> article, but the only way I could make my alignment look like the alignment
> in the article was if I deleted the sequences before a TATA-box. If i didn't
> do the deletion, neither the exons nor introns would match.

If you are considering the comparison of two, relatively short sequences
I recommend using an implementation of the Smith-Waterman alignment algorithm.
For instance, you could use the swat program that comes with the Phrap/phred
package that Phil Green provides (http://www.phrap.org/) or why not the ssearch
program from the good old Bill Pearson FASTA package
(ftp://ftp.virginia.edu:/pub/fasta/).

It would also be worth considering what program the authors of the article you
compare your results to have used; clustalw or some other program? Are there
many sequences aligned in the same picture? In that case, a multiple alignment
technique has been used. A pairwise comparison will not give you the same
results.

Good luck!

// Daniel Nilsson

--
Daniel Nilsson
Sysadmin and student
Dept. of Genetics and Pathlogy, Uppsala University
Mail:   daniel.nilsson at genpat.uu.se
Phone:  +46(0)18 6111077
Snail:  IGP, Rudbeckaboratoriet, 75185 Uppsala









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