**Looking for good Sequence Analysis Software?**

Bernard Murray bernard at elsie.nci.nih.gov
Sun May 4 22:57:24 EST 1997


In article <ahe4-0405971505500001 at newsstand.cit.cornell.edu>, ahe4 at cornell.edu 
says...
>
>I need a high quality program which will quickly align several human and
>mouse genome sequences and highlight differences.  The program will
>probably have to err on the side of false positives so I don't miss any
>sequence variants.  Any hardware platform is fine.  Does anybody have any
>good suggestions?
>Thanks
>-- 
>---King of All College Students---
>"My arrogance extends only as far as my talent demands."
>"We have a threesome every night..
> Me, my wife and my money"-Howard Stern

How about running a full database search (BLAST etc.) using the most
"important" sequence or group of sequences to allow you to choose the
subset of the database that is interesting (you can decide the cutoff
of significance) and then run Clustal, or your favourite alignment
program, to line them all up?  There was also a thread last week on
choosing good "highlighting" programs.
	In my humble opinion Blast/FastA and ClustalW *are* "high
quality" programs....
		Bernard

Bernard Murray, Ph.D.
bernard at elsie.nci.nih.gov (National Cancer Institute, NIH, Bethesda MD, USA)





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