Sequence alignment

Gys de Jongh GysdeJongh at planet.nl
Mon Oct 16 14:03:10 EST 2000

"Ulrik" <Ulriks at ruc.dk> wrote in message
news:8s9lhi$jn6$1 at unlisys.unlisys.net...
> Hi all
> I am a third year molecular biology student (only just started on my third
> year), and I am writing on a project compiling the litterature on a family
> of proteins called connexins.
> I have found only few comparisons between genes coding for the same protein,
> but from different animals. The promotor sequence of one proteine seems to
> be very interesting since it seems to differ greatly from animal to animal,
> though there is a very high degree of homology between exons and introns.
> 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.

ClustalW can align sequences with one or more very large gaps only if you set
the "gap extension penalty" to zero. If you want to make a manual alignment use
Genedoc at http://www.cris.com/~ketchup/genedoc.shtml In this multiple alignment
editor you can use different colors for easy viewing etc. In a dotplot sequence
homology will show up as diagonal lines.

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