GeNT

GeNT is a FORTRAN program that 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.

Gent was originally written by Hugh Nicholas at the Pittsburgh Supercomputing Center. 

Usage on Bridges-2

To see what versions of  GeNT are available and if there is more than one, which is the default, along with some help, type

module spider gent

To use GeNT, include a command like this in your batch script or interactive session to load the GeNT module: (note ‘module load’ is case-sensitive):

module load gent

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
   //