[EMBOSS] Nucleotide profiles with prophecy

[Jon Ison]

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
>
>
>
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