EufindtRNA, on the other hand, only searches for linear sequence signals. The scores for these A and B boxes are then added to a log odds score for the nucleotide distance between the A and B boxes to produce an intermediate score. Finally, a log odds score for the distance to the nearest downstream poly-T pol III termination signal is added to the intermediate score to obtain a final score. If the final score is above a final score cutoff, the tRNA identity and location is saved. These modifications increase the algorithm's sensitivity but greatly reduce EufindtRNA's selectivity.
Cove programs look for tRNAs in a very different way.
A probabilistic model for tRNA has been developed by aligning known tRNAs and giving a base-specific probability score to every nucleotide in the tRNA model. Cove applies this probabilistic model to the entire windowed sequence, and produces a probability score that the sequence matches the tRNA model. The tRNA type is predicted by identifying the anticodon within the structure output. Introns are also automatically identified from the structure output as runs of five or more consecutive non-consensus nucleotides within the anticodon loop. We have observed that tRNAs with low scores for either component of the total score were often pseudogenes.