A Preliminary Study for Solving the Gap Problems in Protein Sequence Alignment-Reference-Cited by-同舟云学术

A Preliminary Study for Solving the Gap Problems in Protein Sequence Alignment

Published:2023-05-02 Issue: Volume: Page:
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Author:

El-Lakkani Ali¹,El-Sherif Seham¹

Affiliation:

1. Cairo University

Abstract

Abstract Protein sequence alignment has many applications in molecular biology. The existing algorithms produce imperfect alignments, because of two factors: 1) the proposed gap penalty function and its parameter values 2) the gap problems. The present work is an attempt to obtain correct alignments using a novel alignment method based on the harmonic identical words present in the sequences to be aligned. To prove the accuracy of this approach, our method is applied to three pairs of sequences. The results are compared with the corresponding results obtained from three alignment programs; the EMBL-EBI EMBOSS Needle program with minimum number of gaps, the MSAEMBL-EBI MUSCLE and Clustal Omega programs. The comparison shows that, in case of highly similar protein sequences the identity and the maximum score value of our alignment method is higher than that of the EMBL-EBI EMBOSS Needle, MUSCLE and Clustal Omega programs. In case of distantly related sequences, the maximum score value of our alignment is much higher than that of the EMBL-EBI EMBOSS Needle, MUSCLE and Clustal Omega programs and the obtained percent identity is shifted from the twilight zone to the safe zone.Our results also show that the gap lengths distribution follows a power law, and this is not achieved by many current alignment programs.

Publisher

Research Square Platform LLC

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