Samira-VP: A simple protein alignment method with rechecking the alphabet vector positions

Samira Fotoohifiroozabadi, Mohd Saberi Mohamad, Safaai Deris

Research output: Contribution to journalArticlepeer-review

Abstract

Protein structure alignment and comparisons that are based on an alphabetical demonstration of protein structure are more simple to run with faster evaluation processes; thus, their accuracy is not as reliable as three-dimension (3D)-based tools. As a 1D method candidate, TS-AMIR used the alphabetic demonstration of secondary-structure elements (SSE) of proteins and compared the assigned letters to each SSE using the n-gram method. Although the results were comparable to those obtained via geometrical methods, the SSE length and accuracy of adjacency between SSEs were not considered in the comparison process. Therefore, to obtain further information on accuracy of adjacency between SSE vectors, the new approach of assigning text to vectors was adopted according to the spherical coordinate system in the present study. Moreover, dynamic programming was applied in order to account for the length of SSE vectors. Five common datasets were selected for method evaluation. The first three datasets were small, but difficult to align, and the remaining two datasets were used to compare the capability of the proposed method with that of other methods on a large protein dataset. The results showed that the proposed method, as a text-based alignment approach, obtained results comparable to both 1D and 3D methods. It outperformed 1D methods in terms of accuracy and 3D methods in terms of runtime.

Original languageEnglish
Article number1750004
JournalJournal of Bioinformatics and Computational Biology
Volume15
Issue number2
DOIs
Publication statusPublished - Apr 1 2017
Externally publishedYes

Keywords

  • 1D alignment method
  • artificial intelligence
  • bioinformatics
  • dynamic programming
  • Protein structure
  • secondary structure element
  • structure alignment

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

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