PFTOOLs Question

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Hel
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PFTOOLs Question

Post by Hel » Mon Jun 02, 2008 1:43 pm

Hi,

Has anyone any experience for using PFTOOLs (generalized HMMs) for nucleotide sequence motifs? While the original publication states, that the program is able to use DNA/RNA alignments for creating profile files, I do not see any option to build a profile out of a non amino acid alignment.
(I know, that I could use the 6ft program to translate my dna sequences into all six reading frames, but that would increase my profile dataset from 400mb to 1600mb. Building PROSITE profiles out of HMMs isn't a solution either, because I'm kind of comparing HMM search results to pfscan search results.)
The version I'm working with is the 2.3, I tried a downgrade to the 1.0 but that one doesn't compile with any fortran compiler I tried.

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