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Best Match Calculation for GenBank Entries Using tRFs and Sequence Peaks

This document details the process of finding the best match for GenBank entries defined by a polygon of sequence-derived tRFs. We examine the results of AluI and Bme1390I peaks, calculating scores for each peak to assess the best match. The methods include calculating cumulative scores and making decisions on whether to discard peaks based on their matching scores with additional enzymes considered. This experimental data aims to refine the scoring criteria for tRFs in biological sequence analysis.

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Best Match Calculation for GenBank Entries Using tRFs and Sequence Peaks

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  1. find best match find best match reference data base experimental data GenBank Entry A(defined by polygon of sequence derived tRFs) AluI add A to results peak Alu.1 AluI find best match calculate score peak Alu.2 Yes peak Alu.3 Bme1390I ... match > 2/3 ? calculate score score sum Bsh1236I Bme1390I No calculate score peak Bme.1 discard A peak Bme.2 peak Bme.3 GenBank Entry B(defined by polygon of sequence derived tRFs) ... add B to results AluI find best match calculate score Yes Bsh1236I Bme1390I match > 2/3 ? peak Bsh.1 calculate score find best match score sum peak Bsh.2 Bsh1236I peak Bsh.3 No calculate score find best match ... discard B (+ additional enzymes, up to 13)

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