HOW TO DEAL WITH SMALL OPEN READING FRAMES?

Current 'classical' algorithms recognizing protein coding sequences do not work effectively with sequences of small length. To deal with this problem we have proposed some improvements of the existing gene finders without any assumed arbitrary threshold. Introduced parameters describe position of tested sequences in the ranking of all small Open Reading Frames and short protein coding genes found in the analyzed genome. The sequences can be ranked according to the coding potential calculated by 'standard' gene prediction algorithms. As an example, we used two algorithms for gene recognition and tested the set of selected small ORFs which were selected from prokaryotic genomes using sequence similarity methods. The applied approach enabled to identify promising sequence that can code for small proteins.