[EMBOSS] Nucleotide profiles with prophecy

[Yasser El-Manzalawy]

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