need aligner help
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:
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.
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