TMATCH: A New Algorithm for Protein Alignments using amino-acid hydrophobicities [article]

David P Cavanaugh, Krishnan Chittur
2019 bioRxiv   pre-print
The identification of proteins of similar structure using sequence alignment is an important problem in bioinformatics. We describe TMATCH, a basic dynamic programming alignment algorithm which can rapidly identify proteins of similar structure from a database. TMATCH was developed to utilize an optimal hydrophobicity metric for alignments traceable to fundamental properties of amino-acids. Standard alignment algorithms use affine gap penalties as contrasted with the TMATCH algorithm adaptation
more » ... of local alignment score reinforcement of favorable diagonal paths (transitions) and punishment of unfavorable transitions paired with fixed gap opening penalties. The TMATCH algorithm is especially designed to take advantage of the extra information available within the hydrophobicity scale to detect homologies, as opposed to the probabilities derived from raw percent identities.
doi:10.1101/2019.12.16.878744 fatcat:nw3ryl43drgejfn3cxezj5eati