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Literature DB >> 15593399

Intergenic sequence inspector: searching and identifying bacterial RNAs.

Abstract

Intergenic Sequence Inspector (ISI) is a program that helps in identifying bacterial ribonucleic acids (RNAs). It automatically extracts, selects and visualizes candidate intergenic regions (IGRs) that bear conservations between phylogenetically related species, displaying sequence and structural signatures of RNA genes encompassing putative promoters, terminators, RNA secondary structure predictions and the G+C percent of the selected sequences. ISI is intentionally modular to analyze various bacterial genomes according to their intrinsic specificities and to the available data. ISI provides a sum of information to the user who can evaluate whether or not an IGR is susceptible to express RNAs.

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Year: 2003 PMID： 15593399 DOI： 10.1093/bioinformatics/btg235

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

14 in total

1. Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains.

Authors: Christophe Pichon; Brice Felden
Journal: Proc Natl Acad Sci U S A Date: 2005-09-23 Impact factor: 11.205

2. A comparative study of sequence- and structure-based features of small RNAs and other RNAs of bacteria.

Authors: Amita Barik; Santasabuj Das
Journal: RNA Biol Date: 2017-11-13 Impact factor: 4.652

3. sRNAscanner: a computational tool for intergenic small RNA detection in bacterial genomes.

Authors: Jayavel Sridhar; Narmada Sambaturu; Suryanarayanan Ramkumar Narmada; Radhakrishnan Sabarinathan; Hong-Yu Ou; Zixin Deng; Kanagaraj Sekar; Ziauddin Ahamed Rafi; Kumar Rajakumar
Journal: PLoS One Date: 2010-08-05 Impact factor: 3.240

4. An in silico model for identification of small RNAs in whole bacterial genomes: characterization of antisense RNAs in pathogenic Escherichia coli and Streptococcus agalactiae strains.

Authors: Christophe Pichon; Laurence du Merle; Marie Elise Caliot; Patrick Trieu-Cuot; Chantal Le Bouguénec
Journal: Nucleic Acids Res Date: 2011-12-01 Impact factor: 16.971

5. A genome-wide identification analysis of small regulatory RNAs in Mycobacterium tuberculosis by RNA-Seq and conservation analysis.

Authors: Danilo Pellin; Paolo Miotto; Alessandro Ambrosi; Daniela Maria Cirillo; Clelia Di Serio
Journal: PLoS One Date: 2012-03-28 Impact factor: 3.240

6. Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics.

Authors: Coral del Val; Elena Rivas; Omar Torres-Quesada; Nicolás Toro; José I Jiménez-Zurdo
Journal: Mol Microbiol Date: 2007-10-25 Impact factor: 3.501

Intergenic sequence inspector: searching and identifying bacterial RNAs.

1. Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains.

2. A comparative study of sequence- and structure-based features of small RNAs and other RNAs of bacteria.

3. sRNAscanner: a computational tool for intergenic small RNA detection in bacterial genomes.

4. An in silico model for identification of small RNAs in whole bacterial genomes: characterization of antisense RNAs in pathogenic Escherichia coli and Streptococcus agalactiae strains.

5. A genome-wide identification analysis of small regulatory RNAs in Mycobacterium tuberculosis by RNA-Seq and conservation analysis.

6. Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics.

7. De novo computational prediction of non-coding RNA genes in prokaryotic genomes.

8. PresRAT: a server for identification of bacterial small-RNA sequences and their targets with probable binding region.

9. Computational small RNA prediction in bacteria.

10. Novel regulatory small RNAs in Streptococcus pyogenes.