need aligner help

Bill Pearson wrp at cyclops.micr.Virginia.EDU
Thu May 28 09:15:04 EST 1992

In article <1992May27.231828.1129 at newssun.med.miami.edu> emansell at miasun.med.miami.edu (eric mansell) writes:
>I'm trying to locate an alignment program that will run
>on a Mac (any kind 'ceptin the Quadra) and  displays the
>entire sequence of the first entry and indicates
>sequence identity in any subsequent entries with a "-", 
>instead of the actual character at that position.
>	For example... seq1 MAELAVIR
>	               seq2 --A---V-
>	instead of...  seq1 MAELAVIR
> 		       seq2 MAaLAVvR

	The programs in the FASTA program package do this with a
command line option (including the Mac version, the GCG modified
version may not). If you type:

	fasta -m 2
and answer the prompts for filename and library (or sequence filename), you
will get alignments that look like:

           seq1 MAELAVIR
	   seq2 ..A...V.

which can easily be edited to change '.' to '-'.

Other programs in the fasta package, such as align (global alignment) and
ssearch (smith-waterman best local alignment) use the same convention.

Bill Pearson

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