Publication detail

The identification of replication origin in bacterial genomes by cumulated phase signal

MADĚRÁNKOVÁ, D. SEDLÁŘ, K. VÍTEK, M. ŠKUTKOVÁ, H.

Original Title

The identification of replication origin in bacterial genomes by cumulated phase signal

English Title

The identification of replication origin in bacterial genomes by cumulated phase signal

Type

conference paper

Language

en

Original Abstract

The origin of replication (oriC) plays an important role in the cell cycle as the place where DNA replication is initiated. In bacterial cells, a single replication origin can be found and its correct identification is necessary in the annotation process of newly sequenced genomes. Although the rearrangement of a whole genome sequence according to oriC should be a standard procedure, public databases still contain lots of genomes starting at a random place. This situation complicates the comparative analysis of whole bacterial genomes as only two genomes rearranged according to oriC can be reliably aligned. In this paper, we present a novel technique for oriC prediction based exclusively on utilization of cumulated phase signal which distinguishes our approach from current techniques combining application of genomic signal processing techniques with a standard character based comparison. Proposed technique is therefore fast and suitably complements the current pipeline for comparison of whole bacterial genomes by aligned downsampled signals.

English abstract

The origin of replication (oriC) plays an important role in the cell cycle as the place where DNA replication is initiated. In bacterial cells, a single replication origin can be found and its correct identification is necessary in the annotation process of newly sequenced genomes. Although the rearrangement of a whole genome sequence according to oriC should be a standard procedure, public databases still contain lots of genomes starting at a random place. This situation complicates the comparative analysis of whole bacterial genomes as only two genomes rearranged according to oriC can be reliably aligned. In this paper, we present a novel technique for oriC prediction based exclusively on utilization of cumulated phase signal which distinguishes our approach from current techniques combining application of genomic signal processing techniques with a standard character based comparison. Proposed technique is therefore fast and suitably complements the current pipeline for comparison of whole bacterial genomes by aligned downsampled signals.

Keywords

cumulated phase, origin of replication, oriC, genomic signal, bacteria

Released

05.10.2017

Publisher

IEEE

ISBN

978-1-4673-8988-4

Book

2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)

Pages from

1

Pages to

5

Pages count

5

URL

BibTex


@inproceedings{BUT140330,
  author="Denisa {Maděránková} and Karel {Sedlář} and Martin {Vítek} and Helena {Škutková}",
  title="The identification of replication origin in bacterial genomes by cumulated phase signal",
  annote="The origin of replication (oriC) plays an important role in the cell cycle as the place where DNA replication is initiated. In bacterial cells, a single replication origin can be found and its correct identification is necessary in the annotation process of newly sequenced genomes. Although the rearrangement of a whole genome sequence according to oriC should be a standard procedure, public databases still contain lots of genomes starting at a random place. This situation complicates the comparative analysis of whole bacterial genomes as only two genomes rearranged according to oriC can be reliably aligned. In this paper, we present a novel technique for oriC prediction based exclusively on utilization of cumulated phase signal which distinguishes our approach from current techniques combining application of genomic signal processing techniques with a standard character based comparison. Proposed technique is therefore fast and suitably complements the current pipeline for comparison of whole bacterial genomes by aligned downsampled signals.",
  address="IEEE",
  booktitle="2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)",
  chapter="140330",
  doi="10.1109/CIBCB.2017.8058561",
  howpublished="online",
  institution="IEEE",
  year="2017",
  month="october",
  pages="1--5",
  publisher="IEEE",
  type="conference paper"
}