question about prophecy and profit

[Jan T. Kim]

On Wed, Mar 26, 2003 at 03:21:26PM +0000, Jane Fowler wrote:

> I  am  trying  to  use  the  prophecy  and profit programs to locate a
> consensus  sequence  in  a genome. I am wondering if it is possible to
> use  a  DNA  sequence  or if it must be a protein sequence to create a
> frequency matrix. It would be great if someone could reply.

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I've run into the same question some time ago and found out that, prophecy
and profit do not care at all what type of sequence (amino acid or
nucleotide) is processed. In fact, these programs seem to operate
generically on sequences of the letters a-z, in the source, I found no
indication that the programs make any specific assumptions on what these
letters denote biologically. The matrices produced by prophecy have
26 columns, not 20 for the amino acids (as I originally thought before
I tried counting instead of thinking...  ;-)  )

The bottom line is: You can use prophecy and profit on any type of
sequence, but note that you'll get nonsense if your sequences contain
ambiguity codes (such as R for purine, Y for pyrimidine etc.).

Greetinx, Jan
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