Very Fast Identi cation of tRNA in Genomic DNA

The identication of functional regions in genomic DNA increasingly relies on the coupling of experimental work to computer processing of sequences. Newly sequenced fragments of a genome may be analysed with computer programs and the result of an automated search may guide a new set of experiments. In such a context, this paper focuses on the identication of tRNA sequences. The role of tRNA in protein synthesis is of key importance. Over the last 20 years, the tRNA molecule has been extensively studied. The corresponding gene is a short sequence which folds in the form of a clover leaf. A large amount of sequences are available and aligned [1]. Conserved regions appear in the alignment which consists in only 76 positions. There are basically two approaches to the identication of tRNA genes. It is either part of a general purpose method designed for searching and/or folding RNA sequences [2, 3, 4] or a self-contained method tailor made for searching tRNA genes such as [5, 6]. As one can expect, reported results are usually more accurate in the latter case. Whatever the approach, priority is rarely given to how quickly a search is performed. Nevertheless , within years, complete genomes of various organisms will be available and fast sequence scanning is already becoming a concern. The rst really reliable algorithm, tRNAscan [5] is based on the use of "weight" or "con-sensus" matrices which make the denition of the RNA motifs more exible and is often part of a general search strategy [7].The algorithm depends on two essential characteristics of the primary and secondary structure of the tRNA gene: (1) the presence of invariant (i.e. universal) and semi-invariant nucleotides located in two highly conserved regions, (2) the clover leaf structure consisting in four arms (paired bases) and three loops (unpaired bases), one of which being of variable size. Such an approach was pushed further to improve both the exibility and the speed of the algorithm. To address the question of exibility, in particular in dening arms, each of the possible ten pairs (regardless of the orientation) is given a weight. These values re BLOCKINect the