ClustalW problem

Doug Eernisse DEernisse at fullerton.edu
Wed Dec 2 17:49:39 EST 1998

In article <bpmurray*STUFFER*-0112981801300001 at mac-daddy.ucsf.edu>,
bpmurray*STUFFER*@socrates.ucsf.edu (Bernard P. Murray, PhD) wrote:

> Hello there,
>      I'm using ClustalW 1.74 for the Mac to compare protein database
> sequences to weed out redundant/repeated occurrences.  I use the
> default parameters and prepare the multiple sequence file in a
> random order.  One strange thing I found was that when I tried to
> align two identical sequences (296 aa) with two somewhat scrambled but
> somewhat related fragments (eg. 100 aa) Clustal completely failed to
> spot the identical nature of the two long forms and "aligned" them in
> a very staggered manner.  I had thought that the initial clustering
> was designed to stop these things happening.  Normally Clustal (since
> version W) has behaved impeccably for me and happily aligns sequences
> with big disparities in length (eg. a plasmid+insert sequence with
> a small piece of the insert) so I was surprised to see this.
>      Changing the order of the sequences in the file did not help.
> Has anyone else come across this and how did you cope?
> (ie. can you juggle the parameters or do you have to
> perform pairwise alignments before constructing the multiple
> sequence file?)
> I'll test the same input file tonight with the DOS and Linux
> versions just to make sure its not a Mac-specific effect.
>      Curious,
>           Bernard
> -- 
> Bernard P. Murray, PhD
> Dept. Cell. Mol. Pharmacol., UCSF, San Francisco, USA

Not sure about the answer to your question, but perhaps you were
unaware of the newer interface for Clustal W called Clustal X.
It is much nicer to use, although the most current Mac PPC version seems
to be 1/98 (1.64) so perhaps your Clustal W is newer. See:





Let us know when you figure out what is going on. That sounds odd.


Doug Eernisse
Department of Biological Science
California State University
Fullerton, CA 92834-6850 USA

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