Predicting sRNA genes in the genome of E.coli by the promoter-search algorithm PlatProm

被引：3

作者：

Brok-Volchanski, AS

Masulis, IS

Shavkunov, KS

Lukyanov, VI

Purtov, YA

Kostyanicina, EG

Deev, AA

Ozoline, ON ^{[1
]}

机构：

[1] Russian Acad Sci, Inst Cell Biophys, Pushchino 142290, Moscow Region, Russia

[2] Russian Acad Sci, Inst Theorat & Experimental Biophys, Pushchino 142290, Moscow Region, Russia

来源：

BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE II | 2006年

关键词：

promoters; genome regulatory regions; gene expression; promoter-search software; transcription; untranslated RNAs; genome annotation;

D O I：

10.1007/0-387-29455-4_2

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The potentially transcribed regions in the genome of E. coli were searched for on a systematic basis using the novel pattern recognition software PlatProm. PlatProm takes into consideration both the sequence-specific and structure-specific features in the genetic environment of the promoter sites and identifies transcription start points with a very high accuracy. The whole genome scanning by PlatProm along with the expected promoters upstream of the annotated genes identified several hundred of very similar signals in other intergenic regions and in many coding sequences. Most of them are expected as start points for independent RNA transcripts, providing a unique opportunity to reveal genes encoding antisense and/or alternative RNAs. The potential PlatProm as a tool revealing sRNA genes is discussed.

引用

页码：11 / 20

页数：10