Multiple alignment of protein sequences

Donald A. Lehn donnel at
Wed Feb 5 16:27:16 EST 1992

In article <1992Feb5.202309.22818 at> umbjs at (Jean Starkey) writes:
/>	I would like to know the programs that will
/>allow me align primary sequences of polypeptides of
/>about 400 amino acids long, to see if there any 
/>significant homology.  I have used FASTA and BESTFIT
/>and other programs on the GCG package available on
/>the front end of the Pittsburg super computer. 
/>	Unfortunately, these programs allow one to
/>align only two sequences at a time.  I have seen 
/>many papers in which more than half a dozen of 
/>sequences aligned.  If any one on the net has any
/>information about such programs please let me know
/>at the following E-mail address.  I need a program 
/>that aligns at least five to six different protein
/>	Thank you very much in advance.
/>Rajani Bommakanti
/>E-mail   bommakan at
/>			or
/>	 uchajbk at mtsunix1
/>phone #  406-587-8906 (home-message)
/>	 406-994-3926 (lab)

There is an excellent program for doing this called: MACAW (Multiple Alignment
Construction & Analysis Workbench).  This is a MS-Windows program that was
written by Gregory D. Schuler of the National Center for Biotechnology
Information.  You can get a copy of it from by anonymous
FTP.  Look for the file macaw***.zip where *** refers to the current version

Donald A. Lehn, Ph.D.                      Phone: (301) 496-2885
Bldg.37 Rm 3D20                            FAX:   (301) 496-8419
National Cancer Institute / NIH            Email: donnel at
Bethesda MD 20892

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