_PROBLEM CoEPrA-2006_Classification_003

_GROUP_NAME Levon Budagyan

_GROUP_MEMBERS
Levon Budagyan

_ADDRESS
levon@molsoft.com;

Levon Budagyan
3366 N. Torrey Pines Ct.,
La Jolla, CA, 92037,
USA;

Molsoft (www.molsoft.com)

_MODELING_PROCEDURE
We used gapped pair counts as descriptors and an SVM classifier as a
prediction method.
  The gapped pair count vector of a sequence with gap length >=0 is a
vector with coordinates indexed by sequence alphabet symbol pairs, i.e.
it has
26 x 26 coordinates, one for each pair of letters.
For each pair the corresponding vector component
  contains the quantity of such ordered pairs with a given gap between
them. E.g. for gap length
l=2 and alphabet pair (A,A), the corresponding vector
component will contain the number of A**A subsequences in
the sequence, where * stands for any symbol.
  Descriptor vectors were composed from the pair count vectors with
different gaps. We concatenated the pair count vectors for the gap 
sizes
from
0 up to some gap length l0 (we used l0=3).
Totally, we had m = 26^2 (l0+1) components in each sequence
  descriptor vector.

SVM classifier with dot kernel was used.

All data transformations and analysis were performed using the
ICM Pro 3.4 program (http://www.molsoft.com/icm_pro.html).

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