Protein sequence comparison based on K-string dictionary

Chenglong Yu, Rong L. He, Stephen S.T. Yau

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

The current K-string-based protein sequence comparisons require large amounts of computer memory because the dimension of the protein vector representation grows exponentially with K. In this paper, we propose a novel concept, the ". K-string dictionary", to solve this high-dimensional problem. It allows us to use a much lower dimensional K-string-based frequency or probability vector to represent a protein, and thus significantly reduce the computer memory requirements for their implementation. Furthermore, based on this new concept, we use Singular Value Decomposition to analyze real protein datasets, and the improved protein vector representation allows us to obtain accurate gene trees.

Original languageEnglish
Pages (from-to)250-256
Number of pages7
JournalGene
Volume529
Issue number2
DOIs
Publication statusPublished - 25 Oct 2013

Keywords

  • Cardinality
  • Frequency vector
  • K-string
  • Sequence comparison
  • Singular Value Decomposition

ASJC Scopus subject areas

  • Genetics

Cite this