Literature DB >> 12468091

A simple and species-independent coding measure.

P Carpena1, P Bernaola-Galván, R Román-Roldán, J L Oliver.   

Abstract

We present a coding measure which is based on the statistical properties of the stop codons, and that is able to estimate accurately the variation of coding content along an anonymous sequence. As the stop codons play the same role in all the genomes (with very few exceptions) the measure turns out to be species-independent. We show results both for prokaryotic and for eukaryotic genomes, indicating, first, the accuracy of the measure, and, second, that better prediction is achieved if the measure is applied on homogeneous, isochore-like sequences than if it is applied following the standard moving window approach. Finally, we discuss on some of the possible applications of the measure.

Mesh:

Substances:

Year:  2002        PMID: 12468091     DOI: 10.1016/s0378-1119(02)01041-7

Source DB:  PubMed          Journal:  Gene        ISSN: 0378-1119            Impact factor:   3.688


  4 in total

1.  IsoFinder: computational prediction of isochores in genome sequences.

Authors:  José L Oliver; Pedro Carpena; Michael Hackenberg; Pedro Bernaola-Galván
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

2.  Predicting statistical properties of open reading frames in bacterial genomes.

Authors:  Katharina Mir; Klaus Neuhaus; Siegfried Scherer; Martin Bossert; Steffen Schober
Journal:  PLoS One       Date:  2012-09-24       Impact factor: 3.240

3.  Deciphering heterogeneity in pig genome assembly Sscrofa9 by isochore and isochore-like region analyses.

Authors:  Wenqian Zhang; Wenwu Wu; Wenchao Lin; Pengfang Zhou; Li Dai; Yang Zhang; Jingfei Huang; Deli Zhang
Journal:  PLoS One       Date:  2010-10-11       Impact factor: 3.240

4.  The random nature of genome architecture: predicting open reading frame distributions.

Authors:  Michael W McCoy; Andrew P Allen; James F Gillooly
Journal:  PLoS One       Date:  2009-07-30       Impact factor: 3.240

  4 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.