Nucleotide profiles with prophecy and profit?

Jan T. Kim kim at
Tue Jan 14 16:07:19 UTC 2003

Dear EMBOSSers,

we have recently attempted to use the programs prophecy and profit with
nucleotide sequences, but we could not figure out how to do this. It
appears that the prophecy program unconditionally assumes amino acid
sequences -- even converting the FASTA formatted file to msf format and
verifying that it says "Type: N" in that, prophecy insists on outputting
a <length> x 20 matrix instead of a <length> x 4 one.

It was also not possible to convince profit to accept a hand-written
<length> x 4 matrix.

Could anyone point out to me how to proceed for search nucleotide sequences
with a profile matrix? I have noticed the tfscan program, but it seems that
employing this would require to construct some kind of mock-up TRANSFAC
around my matrix just so I can scan sequences with that. Probably, I have
overlooked the obvious and now started to think of twisted ways to do such
a scan...?

Thanks in advance for your help.

Greetinx, Jan
 +- Jan T. Kim -------------------------------------------------------+
 |    *NEW*    email: kim at                          |
 |    *NEW*    WWW:    |
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