### 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 language | English (US) |
---|---|

Title of host publication | Computational Genomic Signatures |

Pages | 1-129 |

Number of pages | 129 |

DOIs | |

State | Published - May 31 2011 |

### Publication series

Name | Synthesis Lectures on Biomedical Engineering |
---|---|

Volume | 41 |

ISSN (Print) | 1930-0328 |

ISSN (Electronic) | 1930-0336 |

### Fingerprint

### 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

*Computational Genomic Signatures*(pp. 1-129). (Synthesis Lectures on Biomedical Engineering; Vol. 41). https://doi.org/10.2200/S00360ED1V01Y201105BME041

**Computational genomic signatures.** / Nalbantoglu, Ozkan Ufuk; Sayood, Khalid.

Research output: Chapter in Book/Report/Conference proceeding › Chapter

*Computational Genomic Signatures.*Synthesis Lectures on Biomedical Engineering, vol. 41, pp. 1-129. https://doi.org/10.2200/S00360ED1V01Y201105BME041

}

TY - CHAP

T1 - Computational genomic signatures

AU - Nalbantoglu, Ozkan Ufuk

AU - Sayood, Khalid

PY - 2011/5/31

Y1 - 2011/5/31

N2 - 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.

AB - 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.

KW - Bioinformatics

KW - Classification

KW - Genome

KW - Horizontal gene transfer

KW - Kolmogorov complexity

KW - Markov models

KW - Metagenomics

KW - Minimum description length

KW - Phylogeny

UR - http://www.scopus.com/inward/record.url?scp=79958842021&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79958842021&partnerID=8YFLogxK

U2 - 10.2200/S00360ED1V01Y201105BME041

DO - 10.2200/S00360ED1V01Y201105BME041

M3 - Chapter

SN - 9781608451456

T3 - Synthesis Lectures on Biomedical Engineering

SP - 1

EP - 129

BT - Computational Genomic Signatures

ER -