Dear Yasser The prophecy program is for use with protein sequences only and always interprets its input as protein. I don't think the underlying Gribskov or Henikoff profiles we're ever intended for use with nucleotide sequences.
You could try the new EMBASSY HMMER package, which contains applications that wrap (call) applications for HMM analysis from the latest version of the hmmer suite by Sean Eddy. These too are not recommended for use with nucletotide sequences but would almost certainly work better than the older style profiles. Cheers Jon > Hi, > > I am trying to build a nucleotide profile for the following multiple sequence > alignment: > > !!NA_MULTIPLE_ALIGNMENT > > 30 MSF: 8 Type: N Jul 14, 2006 01:37 Check: 0 .. > > Name: 1 Len: 8 Check: 2489 Weight: 1.00 > Name: 2 Len: 8 Check: 2489 Weight: 1.00 > Name: 3 Len: 8 Check: 2489 Weight: 1.00 > Name: 4 Len: 8 Check: 2489 Weight: 1.00 > Name: 5 Len: 8 Check: 2525 Weight: 1.00 > Name: 6 Len: 8 Check: 2608 Weight: 1.00 > Name: 7 Len: 8 Check: 2608 Weight: 1.00 > Name: 8 Len: 8 Check: 2725 Weight: 1.00 > Name: 9 Len: 8 Check: 2714 Weight: 1.00 > Name: 10 Len: 8 Check: 2616 Weight: 1.00 > Name: 11 Len: 8 Check: 2494 Weight: 1.00 > Name: 12 Len: 8 Check: 2733 Weight: 1.00 > Name: 13 Len: 8 Check: 2436 Weight: 1.00 > Name: 14 Len: 8 Check: 2615 Weight: 1.00 > Name: 15 Len: 8 Check: 2589 Weight: 1.00 > Name: 16 Len: 8 Check: 2705 Weight: 1.00 > Name: 17 Len: 8 Check: 2742 Weight: 1.00 > Name: 18 Len: 8 Check: 2591 Weight: 1.00 > Name: 19 Len: 8 Check: 2640 Weight: 1.00 > Name: 20 Len: 8 Check: 2761 Weight: 1.00 > Name: 21 Len: 8 Check: 2471 Weight: 1.00 > Name: 22 Len: 8 Check: 2744 Weight: 1.00 > Name: 23 Len: 8 Check: 2569 Weight: 1.00 > Name: 24 Len: 8 Check: 2605 Weight: 1.00 > Name: 25 Len: 8 Check: 2593 Weight: 1.00 > Name: 26 Len: 8 Check: 2675 Weight: 1.00 > Name: 27 Len: 8 Check: 2481 Weight: 1.00 > Name: 28 Len: 8 Check: 2658 Weight: 1.00 > Name: 29 Len: 8 Check: 2736 Weight: 1.00 > Name: 30 Len: 8 Check: 2641 Weight: 1.00 > // > > 1 CGTCACGC > 2 CGTCACGC > 3 CGTCACGC > 4 CGTCACGC > 5 GGTCACGG > 6 TGTCATGC > 7 TGTCATGC > 8 AGTCATGT > 9 AGTCACTT > 10 GGTCACTG > 11 TATCACGC > 12 TGTCACTT > 13 AGCCACGC > 14 GATCATGG > 15 CGTTACGG > 16 AGTCTCTG > 17 AGTCGTTG > 18 TGCCACGT > 19 GGTCAGTG > 20 TGTCGTTG > 21 ATTCACAC > 22 GTTCATTG > 23 CATCATAG > 24 TATCAATG > 25 AATGATGC > 26 TAACATGT > 27 AGTCCCGA > 28 CAACATGT > 29 ACTCGCTT > 30 TGATAAGT > > I used the following command line: > prophecy -sequence data.msf -type G -datafile Epprofile -name temp -outfile > profile.prophecy -snucleotide1 > > Although both the input file and the command line indicate that this is > nucleotide sequences, the obtained profile is for protein sequences. > > Could you please, point my to the source of the error? Is it in the data file > or > the command line that I used? > > > Thanks > Yasser EL-Manzalawy > > > > _______________________________________________ > EMBOSS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss > _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
