ClustalW problem

Ashok Aiyar aiyar at ebv.oncology.wisc.edu
Tue Dec 1 23:43:42 EST 1998

On Tue, 01 Dec 1998 18:01:30 -0800,
    Bernard P. Murray, PhD (bpmurray*STUFFER*@socrates.ucsf.edu) wrote:
>Hello there,

Hello Bernard -- First off thank you for sending me your program to
extract sequences from files created by Strider 1.2, and my apologies
for not responding in a more timely fashion.

>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 could not reproduce this using clustalw-1.74 or 1.75 on my Linux
PC.  I used a file that had the following seven sequences:
1 & 4 = human hemoglobin beta chain
2 = horse hemoglobin beta chain
3 = human hemoglobin alpha chain
5 = sea-slug (Aplysia kurodai) myoglobin
6 = horse myoglobin
7 = human myoglobin

Perhaps you have encountered a Mac-specific bug in clustalw-1.74.  BTW,
have you tried this with clustalx?

Ashok Aiyar, Ph.D.
McArdle Laboratory for Cancer Research
aiyar at ebv.oncology.wisc.edu

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