In article <3257099C.2ACDFAD4 at bnl.gov>, jgraves at bnl.gov says...
>>I'm a mathematician just starting to look at multiple sequence alignment
>of DNA. I'm not very familiar with the field and seek references on
>algorithms or survey articles on this subject.
>>We have many thousands of sequences that must be aligned. They include
>quality factors for each base call. Speed is important. We are also
>looking for an algorithm that will find and flag chimeras among these
>sequences.
>>Thanks,
> Janine Graves
> A wonderful program released by Des Higgins and his group is very useful
for multiple alignments of DNA sequences. It is Clustal W, and is available by
ftp at ftp.ebi.ac.uk (I think it's available on a wide range of platforms).
Unfortunately, when dealing with many pieces of DNA, length of each piece plays
a determining role (the maximum alignment Clustal W will allow is 2600bp).
I myself have used this to align rRNA genes (for personal resarch), and
was able to align 70-80 without a problem. However, it did tie the computer up
for a full day (I have a Pentium 150), so it may be better to try a Unix
platform program.
C. J. Fields
University of North Texas
