Literature DB >> 26442194

Bioinformatics as a first-line approach for understanding bacteriophage transcription.

Jelena Guzina1, Marko Djordjevic1.   

Abstract

Current approach to understanding bacteriophage transcription strategies during infection includes a combination of experimental and bioinformatics approaches, which is often time and resource consuming. Given the exponentially growing number of sequenced bacteriophage genomes, it becomes sensible asking to what extent one can understand bacteriophage transcription by using bioinformatics methods alone. We here argue that a suitable choice of computational methods may provide a highly efficient first-line approach for underst-anding bacteriophage transcription.

Entities:  

Keywords:  bacteriophage transcription; bioinformatics analysis; computational genomics; genome analysis; promoter predictions; transcription start-site prediction

Year:  2015        PMID: 26442194      PMCID: PMC4588165          DOI: 10.1080/21597081.2015.1062588

Source DB:  PubMed          Journal:  Bacteriophage        ISSN: 2159-7073


  21 in total

1.  BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes.

Authors:  X Liu; D L Brutlag; J S Liu
Journal:  Pac Symp Biocomput       Date:  2001

2.  Gibbs Recursive Sampler: finding transcription factor binding sites.

Authors:  William Thompson; Eric C Rouchka; Charles E Lawrence
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

3.  Quantitative analysis of a virulent bacteriophage transcription strategy.

Authors:  Marko Djordjevic; Ekaterina Semenova; Boris Shraiman; Konstantin Severinov
Journal:  Virology       Date:  2006-08-02       Impact factor: 3.616

4.  Integrating sequence analysis with biophysical modelling for accurate transcription start site prediction.

Authors:  Marko Djordjevic
Journal:  J Integr Bioinform       Date:  2014-06-23

5.  Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite.

Authors:  Mark Borodovsky; Alex Lomsadze
Journal:  Curr Protoc Microbiol       Date:  2014-02-06

Review 6.  Viruses versus bacteria-novel approaches to phage therapy as a tool against multidrug-resistant pathogens.

Authors:  Tania Mareike Viertel; Klaus Ritter; Hans-Peter Horz
Journal:  J Antimicrob Chemother       Date:  2014-05-28       Impact factor: 5.790

Review 7.  Bacteriophage T4 genome.

Authors:  Eric S Miller; Elizabeth Kutter; Gisela Mosig; Fumio Arisaka; Takashi Kunisawa; Wolfgang Rüger
Journal:  Microbiol Mol Biol Rev       Date:  2003-03       Impact factor: 11.056

8.  Cascades of Sigma factors.

Authors:  R Losick; J Pero
Journal:  Cell       Date:  1981-09       Impact factor: 41.582

9.  Prediction of transcription terminators in bacterial genomes.

Authors:  M D Ermolaeva; H G Khalak; O White; H O Smith; S L Salzberg
Journal:  J Mol Biol       Date:  2000-08-04       Impact factor: 5.469

10.  Inferring bacteriophage infection strategies from genome sequence: analysis of bacteriophage 7-11 and related phages.

Authors:  Jelena Guzina; Marko Djordjevic
Journal:  BMC Evol Biol       Date:  2015-02-02       Impact factor: 3.260

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