GeNT

GeNT is a FORTRAN program that was originally written by Hugh Nicholas at the Pittsburgh Supercomputing Center. It is provided on this github page for people that still find it of value. Here is what the code does:

   This program computes the cross entropy for groups of sequences
   that have been assigned to groups on the basis of biochemical,
   physiological, or other biological property.  The sequence
   assignments are cross-validated, again by the cross entropy
   measure, to check for problems with the alignment or group
   assignment.  Sequences that were initially identified as
   "unclassified" are compared to all of the groups using position
   specific log-odds scores as described by Henikoff and Henikoff.
   Positions in the aligned sequences that are important for
   determining group membership are identified by having a high
   entropy for the entire alignment and a high entropy for one or
   more specific groups.

Sample Group File

Below is a sample group file. Sequences are from uniprot database:

   Problem  pa2_small
   Title  PA2 Sequences.
   Group  One
   sp|P00593|PA21B_BOVIN
   sp|P04417|PA21B_AGKHA
   sp|P14418|PA21B_AGKHP
   sp|P81243|PA21B_BOTJA
   sp|P0CAS3|PA212_CRODR
   sp|P0CAS4|PA213_CRODR
   sp|P0CAS5|PA215_CRODU
   sp|P0CAS6|PA216_CRODU
   sp|P0CAS7|PA217_CRODU
   //
   Group  Two
   sp|P00606|PA20_BUNMU
   sp|Q8UW08|PA20_LAPHA
   sp|P08873|PA20_NOTSC
   sp|P20254|PA20_PSEAU
   sp|Q9PUH4|PA210_AUSSU
   sp|Q9PUH3|PA211_AUSSU
   sp|Q9PUH2|PA212_AUSSU
   sp|Q9PUH1|PA213_AUSSU
   sp|Q9PUH0|PA214_AUSSU
   sp|Q9PUG9|PA215_AUSSU
   sp|Q9PUG8|PA216_AUSSU
   sp|Q9PUG7|PA217_AUSSU
   sp|P81236|PA21B_ACAAN
   sp|P59359|PA21B_AUSSU
   sp|Q8QFW4|PA21B_BUNCE
   sp|Q90WA7|PA21B_BUNFA
   sp|P00617|PA21B_BUNMU
   //

To Compile:

gfortran -o gent gent.for

To run:

gent

Plotting results:

The file gnuplot.script worked with gnuplot to plot program output (plot.data) into a PNG file (plot.png).