Bioinformatics. 2006 Nov 15;22(22):2819-20. Epub 2006 Sep 11.

Augur--a computational pipeline for whole genome microbial surface protein prediction and classification.

Billion A, Ghai R, Chakraborty T, Hain T.

Source

Institute of Medical Microbiology, Justus-Liebig-University Frankfurter Strasse 107, D-35392 Giessen, Germany. Andre.Billion@mikrobio.med.uni-giessen.de

Abstract

The analysis of protein function is a challenge and a major bottleneck towards well-annotated and analysed microbial genomes. In particular, bacterial surface proteins present an opportunity for pharmacological intervention and vaccine development. We present Augur, an automatic prediction pipeline that integrates major surface prediction algorithms and enables comparative analysis, classification and visualization for gram-positive bacteria on a genomic scale. AVAILABILITY: http://bioinfo.mikrobio.med.uni-giessen.de/augur

PMID:: 16966358; [PubMed - indexed for MEDLINE]

Free full text

Publication Types, MeSH Terms, Substances

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

Substances

LinkOut - more resources

Full Text Sources

Other Literature Sources

Labome Researcher Resource - ExactAntigen/Labome

Supplemental Content

Save items

Related citations in PubMed

TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins. [BMC Bioinformatics. 2005]
TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins.
Garrow AG, Agnew A, Westhead DR. BMC Bioinformatics. 2005 Mar 15; 6:56. Epub 2005 Mar 15.
Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria. [BMC Genomics. 2005]
Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria.
Rey S, Gardy JL, Brinkman FS. BMC Genomics. 2005 Nov 17; 6:162. Epub 2005 Nov 17.
Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method. [BMC Bioinformatics. 2005]
Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method.
Bagos PG, Liakopoulos TD, Hamodrakas SJ. BMC Bioinformatics. 2005 Jan 12; 6:7. Epub 2005 Jan 12.
Review Intrinsic disorder and functional proteomics. [Biophys J. 2007]
Review Intrinsic disorder and functional proteomics.
Radivojac P, Iakoucheva LM, Oldfield CJ, Obradovic Z, Uversky VN, Dunker AK. Biophys J. 2007 Mar 1; 92(5):1439-56. Epub 2006 Dec 8.
Review Proteomics--a new player in the post-genomic era. [Indian J Biochem Biophys. 2002]
Review Proteomics--a new player in the post-genomic era.
Maithal K. Indian J Biochem Biophys. 2002 Oct; 39(5):291-302.

See reviews... See all...

Cited by 14 PubMed Central articles

Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome. [BMC Genomics. 2013]
Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome.
Kuenne C, Billion A, Mraheil MA, Strittmatter A, Daniel R, Goesmann A, Barbuddhe S, Hain T, Chakraborty T. BMC Genomics. 2013 Jan 22; 14:47. Epub 2013 Jan 22.
Subcellular localization of extracytoplasmic proteins in monoderm bacteria: rational secretomics-based strategy for genomic and proteomic analyses. [PLoS One. 2012]
Subcellular localization of extracytoplasmic proteins in monoderm bacteria: rational secretomics-based strategy for genomic and proteomic analyses.
Renier S, Micheau P, Talon R, Hébraud M, Desvaux M. PLoS One. 2012; 7(8):e42982. Epub 2012 Aug 9.
Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. [BMC Genomics. 2012]
Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes.
Hain T, Ghai R, Billion A, Kuenne CT, Steinweg C, Izar B, Mohamed W, Mraheil MA, Domann E, Schaffrath S, et al. BMC Genomics. 2012 Apr 24; 13:144. Epub 2012 Apr 24.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Augur--a computational pipeline for whole genome microbial surface protein predi...
Augur--a computational pipeline for whole genome microbial surface protein prediction and classification.
Bioinformatics. 2006 Nov 15 ;22(22):2819-20. Epub 2006 Sep 11 .

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: