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Bioinformatics Vol. 18 no. 2 2002
Pages 343-350
© 2002 Oxford University Press

Translation initiation start prediction in human cDNAs with high accuracy

Artemis G. Hatzigeorgiou 1,2

1 Metagen GmbH, Ihnestr.63, 14195 Berlin-Dahlem, Germany and Synaptic Ltd., Science and Technology Park of Crete, PO Box 1447, Voures Herakleion, 71110 Greece

Received on March 2, 2001 ; revised on October 24, 2001 ; accepted on October 24, 2001

Motivation: Correct identification of the Translation Initiation Start (TIS) in cDNA sequences is an important issue for genome annotation. The aim of this work is to improve upon current methods and provide a performance guaranteed prediction.

Methods: This is achieved by using two modules, one sensitive to the conserved motif and the other sensitive to the coding/non-coding potential around the start codon. Both modules are based on Artificial Neural Networks (ANNs). By applying the simplified method of the ribosome scanning model, the algorithm starts a linear search at the beginning of the coding ORF and stops once the combination of the two modules predicts a positive score.

Results: According to the results of the test group, 94% of the TIS were correctly predicted. A confident decision is obtained through the use of the Las Vegas algorithm idea. The incorporation of this algorithm leads to a highly accurate recognition of the TIS in human cDNAs for 60% of the cases.

Availability: The program is available upon request from the author.

Contact: agh{at}pcbi.upenn.edu

2 Present address: Department of Genetics, University of Pennsylvania, School of Medicine, 1407 Blockley Hall, 418 Guardian Drive, Philadelphia, PA 19104-6021, USA.


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