Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequences

Motivation: In the previous works, we developed ATGpr, a computer program for predicting the fullness of a cDNA, i.e, whether it contains an initiation codon or not. Statistical information of short nucleotide fragments was fully exploited in the prediction algorithm. However sequence similarities to known proteins, which are becoming increasingly available due to recent rapid growth of protein database, were not used in the prediction. In this work, we present a new prediction algorithm based on both statistical and similarity information, which provides better performance in sensitivity and specificity. Results: We evaluated the accuracy of ATGpr for predicting fullness of cDNA sequences from human clustered ESTs of UniGene, and we obtained specificity sensitivity, and correlation coefficient of this prediction. Specificity and sensitivity crossed at 46% over the ATGpr score threshold of 0.33 and the maximum correlation coefficient of 0.34 was obtained at this threshold. Without ATGpr we found it effective to use alignments with known proteins for predicting the fullness of cDNA sequences. That is, specificity increased monotonously as similarity (identity of the alignments) increased. Specificity was achieved greater than 80% if identity was greater than 40%. For more effective prediction of fullness of cDNA sequences we combined the similarity (identity of query sequence) with known proteins and ATGpr score. As a result, specificity became greater than 80% if identity was greater than 20%.