Accurate Microbial Genome Annotation Using an Integrated and User-Friendly Environment for Community Expertise of Gene Functions: The MicroScope Platform

2015 ◽  
pp. 141-169 ◽  
Author(s):  
Eugeni Belda ◽  
David Vallenet ◽  
Claudine Médigue
Keyword(s):  
Genome Annotation ◽  
Microbial Genome ◽  
Gene Functions ◽  
User Friendly

scholarly journals The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

2015 ◽  
Vol 10 (1) ◽  
Author(s):  
Marcel Huntemann ◽  
Natalia N. Ivanova ◽  
Konstantinos Mavromatis ◽  
H. James Tripp ◽  
David Paez-Espino ◽  
...  
Keyword(s):  
Operating Procedure ◽  
Genome Annotation ◽  
Standard Operating Procedure ◽  
Microbial Genome ◽  
Annotation Pipeline ◽  
Standard Operating

scholarly journals IMG ER: a system for microbial genome annotation expert review and curation

2009 ◽  
Vol 25 (17) ◽  
pp. 2271-2278 ◽  
Author(s):  
Victor M. Markowitz ◽  
Konstantinos Mavromatis ◽  
Natalia N. Ivanova ◽  
I-Min A. Chen ◽  
Ken Chu ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Microbial Genome ◽  
Expert Review

scholarly journals MicroScope: a platform for microbial genome annotation and comparative genomics

Database ◽  
2009 ◽  
Vol 2009 ◽  
Author(s):  
D. Vallenet ◽  
S. Engelen ◽  
D. Mornico ◽  
S. Cruveiller ◽  
L. Fleury ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Genome Annotation ◽  
Microbial Genome

scholarly journals SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2056 ◽  
Author(s):  
Yevgeny Nikolaichik ◽  
Aliaksandr U. Damienikan
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Genome Annotation ◽  
Bacterial Genome ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Factor Binding ◽  
A Genome ◽  
Regulatory Information ◽  
User Friendly

The majority of bacterial genome annotations are currently automated and based on a ‘gene by gene’ approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft RotEnterobacteriaceae(PectobacteriumandDickeyaspp.) andPseudomonasspp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome ofPectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of theP. atrosepticumchromosome. Reviewing the annotation in cases where it didn’t fit with regulatory information allowed us to correct product and gene names for over 300 loci.

scholarly journals Microbial genome analysis: the COG approach

2017 ◽  
Vol 20 (4) ◽  
pp. 1063-1070 ◽  
Author(s):  
Michael Y Galperin ◽  
David M Kristensen ◽  
Kira S Makarova ◽  
Yuri I Wolf ◽  
Eugene V Koonin
Keyword(s):  
Genome Analysis ◽  
Metabolic Pathways ◽  
Genome Annotation ◽  
Functional Characterization ◽  
Microbial Genome ◽  
Functional Categories ◽  
Orthologous Genes ◽  
Microbial Genomes ◽  
The Past

Abstract For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis.

scholarly journals Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation

2020 ◽  
Vol 16 (11) ◽  
pp. e1008214
Author(s):  
Jolene Ramsey ◽  
Helena Rasche ◽  
Cory Maughmer ◽  
Anthony Criscione ◽  
Eleni Mijalis ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Phage Genome ◽  
Structural Annotation ◽  
Sequence Comparisons ◽  
User Training ◽  
Computationally Intensive ◽  
Modern Genomic ◽  
Training Need ◽  
User Friendly ◽  
Computational Analyses

In the modern genomic era, scientists without extensive bioinformatic training need to apply high-power computational analyses to critical tasks like phage genome annotation. At the Center for Phage Technology (CPT), we developed a suite of phage-oriented tools housed in open, user-friendly web-based interfaces. A Galaxy platform conducts computationally intensive analyses and Apollo, a collaborative genome annotation editor, visualizes the results of these analyses. The collection includes open source applications such as the BLAST+ suite, InterProScan, and several gene callers, as well as unique tools developed at the CPT that allow maximum user flexibility. We describe in detail programs for finding Shine-Dalgarno sequences, resources used for confident identification of lysis genes such as spanins, and methods used for identifying interrupted genes that contain frameshifts or introns. At the CPT, genome annotation is separated into two robust segments that are facilitated through the automated execution of many tools chained together in an operation called a workflow. First, the structural annotation workflow results in gene and other feature calls. This is followed by a functional annotation workflow that combines sequence comparisons and conserved domain searching, which is contextualized to allow integrated evidence assessment in functional prediction. Finally, we describe a workflow used for comparative genomics. Using this multi-purpose platform enables researchers to easily and accurately annotate an entire phage genome. The portal can be accessed at https://cpt.tamu.edu/galaxy-pub with accompanying user training material.

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