Computational genomic signatures

Ozkan Ufuk Nalbantoglu, Khalid Sayood

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Scopus citations

Abstract

Recent advances in development of sequencing technology has resulted in a deluge of genomic data. In order to make sense of this data, there is an urgent need for algorithms for data processing and quantitative reasoning. An emerging in silico approach, called computational genomic signatures, addresses this need by representing global species-specific features of genomes using simple mathematical models. This text introduces the general concept of computational genomic signatures, and it reviews some of the DNA sequence models which can be used as computational genomic signatures. The text takes the position that a practical computational genomic signature consists of both a model and a measure for computing the distance or similarity between models. Therefore, a discussion of sequence similarity/distance measurement in the context of computational genomic signatures is presented. The remainder of the text covers various applications of computational genomic signatures in the areas of metagenomics, phylogenetics and the detection of horizontal gene transfer.

Original languageEnglish (US)
Title of host publicationComputational Genomic Signatures
Pages1-129
Number of pages129
DOIs
Publication statusPublished - May 31 2011

Publication series

NameSynthesis Lectures on Biomedical Engineering
Volume41
ISSN (Print)1930-0328
ISSN (Electronic)1930-0336

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Keywords

  • Bioinformatics
  • Classification
  • Genome
  • Horizontal gene transfer
  • Kolmogorov complexity
  • Markov models
  • Metagenomics
  • Minimum description length
  • Phylogeny

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Biochemistry
  • Biomedical Engineering

Cite this

Nalbantoglu, O. U., & Sayood, K. (2011). Computational genomic signatures. In Computational Genomic Signatures (pp. 1-129). (Synthesis Lectures on Biomedical Engineering; Vol. 41). https://doi.org/10.2200/S00360ED1V01Y201105BME041