prophecy

prophecy

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prophecy creates a profile matrix file from a nucleic acid or a protein sequence alignment.

Here is a sample session with prophecy:

% prophecy Creates matrices/profiles from multiple alignments Input sequence set: globins.msf Profile type          F : Frequency          G : Gribskov          H : Henikoff Select type [F]: Enter a name for the profile [mymatrix]: globins Enter threshold reporting percentage [75]: Output file [globins.prophecy]:

Mandatory qualifiers (bold if not always prompted):

[-sequence] (seqset)

Sequence set USA.

-type (menu)

Select type.

-name (string)

Enter a name for the profile.

-threshold (integer)

Enter threshold reporting percentage.

-datafile (matrixf)

Scoring matrix.

-open (float)

Gap opening penalty.

-extension (float)

Gap extension penalty.

[-outf] (outfile)

Output filename.