Literature DB >> 18031997

Annotation, comparison and databases for hundreds of bacterial genomes.

Claudine Médigue1, Ivan Moszer.   

Abstract

The multitude of bacterial genome sequences being determined has opened up a new field of research, that of comparative genomics. One role of bioinformatics is to assist biologists in the extraction of biological knowledge from this data flood. Software designed for the analysis and functional annotation of a single genome have, in consequence, evolved towards comparative genomics tools, bringing together the information contained in numerous genomes simultaneously. This paper reviews advances in the development of bacterial annotation and comparative analysis tools, and progress in the design of novel database structures for the integration of heterogeneous biological information.

Mesh：

Year:  2007        PMID： 18031997     DOI： 10.1016/j.resmic.2007.09.009

Source DB:  PubMed          Journal:  Res Microbiol        ISSN： 0923-2508            Impact factor:   3.992


  18 in total

1.  MS/MS networking guided analysis of molecule and gene cluster families.

Authors:  Don Duy Nguyen; Cheng-Hsuan Wu; Wilna J Moree; Anne Lamsa; Marnix H Medema; Xiling Zhao; Ronnie G Gavilan; Marystella Aparicio; Librada Atencio; Chanaye Jackson; Javier Ballesteros; Joel Sanchez; Jeramie D Watrous; Vanessa V Phelan; Corine van de Wiel; Roland D Kersten; Samina Mehnaz; René De Mot; Elizabeth A Shank; Pep Charusanti; Harish Nagarajan; Brendan M Duggan; Bradley S Moore; Nuno Bandeira; Bernhard Ø Palsson; Kit Pogliano; Marcelino Gutiérrez; Pieter C Dorrestein
Journal:  Proc Natl Acad Sci U S A       Date:  2013-06-24       Impact factor: 11.205

2.  EnzymeDetector: an integrated enzyme function prediction tool and database.

Authors:  Susanne Quester; Dietmar Schomburg
Journal:  BMC Bioinformatics       Date:  2011-09-23       Impact factor: 3.169

Review 3.  Database resources for the tuberculosis community.

Authors:  Jocelyne M Lew; Chunhong Mao; Maulik Shukla; Andrew Warren; Rebecca Will; Dmitry Kuznetsov; Ioannis Xenarios; Brian D Robertson; Stephen V Gordon; Dirk Schnappinger; Stewart T Cole; Bruno Sobral
Journal:  Tuberculosis (Edinb)       Date:  2013-01-17       Impact factor: 3.131

4.  DraGnET: software for storing, managing and analyzing annotated draft genome sequence data.

Authors:  Stacy Duncan; Ruchita Sirkanungo; Leslie Miller; Gregory J Phillips
Journal:  BMC Bioinformatics       Date:  2010-02-22       Impact factor: 3.169

5.  Improving pan-genome annotation using whole genome multiple alignment.

Authors:  Samuel V Angiuoli; Julie C Dunning Hotopp; Steven L Salzberg; Hervé Tettelin
Journal:  BMC Bioinformatics       Date:  2011-06-30       Impact factor: 3.169

6.  BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins.

Authors:  Matti Kankainen; Teija Ojala; Liisa Holm
Journal:  BMC Bioinformatics       Date:  2012-02-15       Impact factor: 3.169

Review 7.  Genome-scale models of bacterial metabolism: reconstruction and applications.

Authors:  Maxime Durot; Pierre-Yves Bourguignon; Vincent Schachter
Journal:  FEMS Microbiol Rev       Date:  2008-12-03       Impact factor: 16.408

8.  In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles.

Authors:  Frank P Y Lin; Enrico Coiera; Ruiting Lan; Vitali Sintchenko
Journal:  BMC Bioinformatics       Date:  2009-03-17       Impact factor: 3.169

9.  MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data.

Authors:  David Vallenet; Eugeni Belda; Alexandra Calteau; Stéphane Cruveiller; Stefan Engelen; Aurélie Lajus; François Le Fèvre; Cyrille Longin; Damien Mornico; David Roche; Zoé Rouy; Gregory Salvignol; Claude Scarpelli; Adam Alexander Thil Smith; Marion Weiman; Claudine Médigue
Journal:  Nucleic Acids Res       Date:  2012-11-27       Impact factor: 16.971

10.  GenoList: an integrated environment for comparative analysis of microbial genomes.

Authors:  Pierre Lechat; Laurence Hummel; Sandrine Rousseau; Ivan Moszer
Journal:  Nucleic Acids Res       Date:  2007-11-21       Impact factor: 16.971
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