Questions about Amino acid seq alignments

John Mihic jmihic at wfubcm.edu
Tue Jun 2 10:16:00 EST 1998

In article <6krndk$cih at ustsu10.ust.hk>, netson at hotmail.com says...
>Dear all,
>    Which software can be use to align multiple sequences of amino acid of
>proteins?  The software that can work in Window95, Dos or WWW platform is
>preferred.  I have used ClustalW for win95 in the alignment but I found that
>there are some bugs in ClustalW.   Also, I would like to know how to creat
>the alignment in the multiple sequence .msf  format or FASTA format?  Since
>the file in these format will be edited by GeneDoc.

There is a freeware program available from NCBI called Macaw 
(ftp://ncbi.nlm.nih.gov/pub/macaw/) that runs under Windows (3.1, 95 and NT) 
as well as Mac.  This program allows you to do multiple amino acid or 
nucleotide sequence alignments. It can read in FASTA format files from Entrez 
(http://www3.ncbi.nlm.nih.gov/Entrez/).  I've used the program for a while now 
and like it. It does what I need to do and the price can't be beat.

John Mihic

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