POL III PROMOTER RECOGNITION: brief description of the computer program POLIIISCAN.

The algorithm used in the computer program POLIIISCAN is described in paper:
"THE RELATION BETWEEN THE STRUCTURE OF THE tRNA GENE PROMOTERS AND tRNA AMINO ACID SPECIFICITY"
Y.V.Kondrakhin (*), I.B.Rogozin, T.M.Naykova, N.S.Yudin, M.I.Voevoda, A.G.Romaschenko.
(*): E.mail address is kondrat@bionet.nsc.ru
Animal Molecular Genetics Laboratiry ,  Institute of Cytology and genetics, Novosibirsk, Russia.
This paper is submitted to the BIOINFORMATICS.

Abstract:
A new method for the recognition of type 2 promoters in the eukaryotic tRNA genes, which takes into consideration not only nucleotide distribution at individual box positions, but also the multiple interactions between the different parts of the boxes is proposed. The recognition system is determined by the module organization of the A and B boxes within intragenic promoters of the tRNA genes.


Recognition procedure was constructed on the base of analysis of the A/B box samples. These samples were composed by applying the developed alignment algorithm to the set of sequences in Compilation of tRNA sequences .

Two samples are available:
The A box
The B box

Select an subject of recognition:

Select 1-st threshold for the A-box recognition:

Select 2-nd threshold for the A-box recognition:

Select the threshold for the B-box recognition:

Enter sequence in plain format 
from Screen (cut & paste)...

from File:

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Author: Y.V.Kondrakhin, I.B.Rogozin, T.M.Naykova, N.S.Yudin, M.I.Voevoda 
Contributors: Sergey V. Lavryushev
Leader: A.G.Romaschenko

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