Multiple alignment of protein sequences

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


In article <1992Feb5.202309.22818 at coe.montana.edu> umbjs at cs.montana.edu (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
/>sequences.
/>	Thank you very much in advance.
/>
/>
/>Rajani Bommakanti
/>
/>E-mail   bommakan at hydrogen.oscs.montana.edu
/>
/>			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 ncbi.nlm.nih.gov by anonymous
FTP.  Look for the file macaw***.zip where *** refers to the current version
number.

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




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