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WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads

Wolfgang Gerlach, Sebastian Jünemann, Felix Tille, Alexander Goesmann, Jens Stoye
2009 BMC Bioinformatics  
Results: In this paper, we introduce WebCARMA, a refined version of CARMA available as a web application for the taxonomic and functional classification of unassembled (ultra-)short reads from metagenomic  ...  Conclusions: We show that unassembled reads as short as 35 bp can be used for the taxonomic classification of a metagenome. The web application is freely available at http://  ...  Acknowledgements WG was supported by the DFG Graduiertenkolleg 635 Bioinformatik, SJ by the BMBF PathoGeno-Mik Plus network project 0313801N and FT by the BMBF ERA-NET PathoGenoMics project 0313939A.  ... 
doi:10.1186/1471-2105-10-430 pmid:20021646 pmcid:PMC2801688 fatcat:lpcwhuwrozbzhe7kb2hgyrrtom

Taxonomic classification of metagenomic shotgun sequences with CARMA3

Wolfgang Gerlach, Jens Stoye
2011 Nucleic Acids Research  
Here we present CARMA3, a new method for the taxonomic classification of assembled and unassembled metagenomic sequences that has been adapted to work with both BLAST and HMMER3 homology searches.  ...  Over the past few years, different methods have been developed for the taxonomic and functional characterization of metagenomic shotgun sequences.  ...  CARMA (9) as well as WebCARMA (10) , a refined version of CARMA available as a web application for the taxonomic and functional classification of metagenomic reads belong to the HMM-based methods.  ... 
doi:10.1093/nar/gkr225 pmid:21586583 pmcid:PMC3152360 fatcat:zltjmmmraze3zpsl5d4r7ydoxi

Taxonomic Classification of Metagenomic Shotgun Sequences with CARMA3 [chapter]

Wolfgang Gerlach, Jens Stoye
2015 Encyclopedia of Metagenomics  
Here we present CARMA3, a new method for the taxonomic classification of assembled and unassembled metagenomic sequences that has been adapted to work with both BLAST and HMMER3 homology searches.  ...  Over the past few years, different methods have been developed for the taxonomic and functional characterization of metagenomic shotgun sequences.  ...  CARMA (9) as well as WebCARMA (10) , a refined version of CARMA available as a web application for the taxonomic and functional classification of metagenomic reads belong to the HMM-based methods.  ... 
doi:10.1007/978-1-4899-7478-5_751 fatcat:a3bnbrexqvc57awtfshz2pzcz4

Taxonomic Classification of Metagenomic Shotgun Sequences with CARMA3 [chapter]

Wolfgang Gerlach, Jens Stoye
2013 Encyclopedia of Metagenomics  
Here we present CARMA3, a new method for the taxonomic classification of assembled and unassembled metagenomic sequences that has been adapted to work with both BLAST and HMMER3 homology searches.  ...  Over the past few years, different methods have been developed for the taxonomic and functional characterization of metagenomic shotgun sequences.  ...  CARMA (9) as well as WebCARMA (10) , a refined version of CARMA available as a web application for the taxonomic and functional classification of metagenomic reads belong to the HMM-based methods.  ... 
doi:10.1007/978-1-4614-6418-1_751-2 fatcat:7aeziiansrcy7paqep3jp5k7li

Mixture models for analysis of the taxonomic composition of metagenomes

Peter Meinicke, Kathrin Petra Aßhauer, Thomas Lingner
2011 Computer applications in the biosciences : CABIOS  
Motivation: Inferring the taxonomic profile of a microbial community from a large collection of anonymous DNA sequencing reads is a challenging task in metagenomics.  ...  Because existing methods for taxonomic profiling of metagenomes are all based on the assignment of fragmentary sequences to phylogenetic categories, the accuracy of results largely depends on fragment  ...  ACKNOWLEDGEMENT We would like to thank Peter Gumrich for programming the Taxy tool for Windows and Christian Opitz, Stefanie Mühlhausen and Alexander Kaever for additional technical support.  ... 
doi:10.1093/bioinformatics/btr266 pmid:21546400 pmcid:PMC3106201 fatcat:is652mryjvc53fn4i4patopt7q

The Microbiome of Brazilian Mangrove Sediments as Revealed by Metagenomics

Fernando Dini Andreote, Diego Javier Jiménez, Diego Chaves, Armando Cavalcante Franco Dias, Danice Mazzer Luvizotto, Francisco Dini-Andreote, Cristiane Cipola Fasanella, Maryeimy Varon Lopez, Sandra Baena, Rodrigo Gouvêa Taketani, Itamar Soares de Melo, A. Mark Ibekwe
2012 PLoS ONE  
Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology.  ...  The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples.  ...  Silva for his help with the mangrove expeditions and sampling. Author Contributions  ... 
doi:10.1371/journal.pone.0038600 pmid:22737213 pmcid:PMC3380894 fatcat:fy5wk377ezdghg6egfk6cn4ecm

Metagenomic Approach: Transforming In-Silico Research for Improved Biogas Production

Roushney Fatima Mukti, Sanjida Sakhawat Sinthee
2019 International Journal of Applied Sciences and Biotechnology  
The composition and gene content of a biogas-producing consortium can be determined through metagenomic approach which allows the design of the optimal microbial community structure for any biogas plant  ...  The structure and function of microbial communities and the effects of the addition of trace elements are needed to be known, to control and channel the energy sources microbes produce and to capture and  ...  WebCARMA is a refined version of CARMA available as a web application for the taxonomic and functional classification of unassembled ultra-short reads from metagenomic communities (Gerlach et al., 2009  ... 
doi:10.3126/ijasbt.v7i1.23315 fatcat:war2u5ygrrg4torfs2s37y5r5q

An introduction to the analysis of shotgun metagenomic data

Thomas J. Sharpton
2014 Frontiers in Plant Science  
Shotgun metagenomic DNA sequencing is a relatively new and powerful environmental sequencing approach that provides insight into community biodiversity and function.  ...  But, the analysis of metagenomic sequences is complicated due to the complex structure of the data.  ...  While protein family classification of metagenomic reads is a useful way of inferring community function, it is imperfect.  ... 
doi:10.3389/fpls.2014.00209 pmid:24982662 pmcid:PMC4059276 fatcat:syz36kyuq5bizjgs4onulfrs3u

Taxonomic binning of metagenome samples generated by next-generation sequencing technologies

J. Droge, A. C. McHardy
2012 Briefings in Bioinformatics  
One of the essential steps in metagenome analysis is reconstruction of draft genomes for populations of a community or of draft 'pan-genomes' for higher level clades.  ...  'Taxonomic binning' corresponds to the process of assigning a taxonomic identifier to sequence fragments, based on information such as sequence similarity, sequence composition or read coverage.  ...  Acknowledgements The authors thank Chris Quince and Alex Scyrba for providing comments.  ... 
doi:10.1093/bib/bbs031 pmid:22851513 fatcat:cklclk6kpfejfpcgliw53lxi4i

Use of Whole Genome Shotgun Metagenomics: A Practical Guide for the Microbiome-Minded Physician Scientist

Jun Ma, Amanda Prince, Kjersti Aagaard
2014 Seminars in Reproductive Medicine  
With the generation of vast amounts of data, the bioinformatics and computational analysis of WGS results become vital for the success of a metagenomics study.  ...  However, each step in the WGS data analysis, including metagenome assembly, gene prediction, taxonomy identification, function annotation, and pathway analysis, is complicated by the shear amount of data  ...  MG-RAST 55 is a comprehensive web tool for both phylogenetic and functional summaries.  ... 
doi:10.1055/s-0033-1361817 pmid:24390915 fatcat:sxkkwrazdrcibl7nzyp44o35c4

A comparative evaluation of sequence classification programs

Adam L Bazinet, Michael P Cummings
2012 BMC Bioinformatics  
We also evaluated the performance of the leading programs in each category on data sets whose taxonomic and functional composition is known.  ...  Due to the sheer number and complexity of methods, it can be difficult for a researcher to choose one that is well-suited for a particular analysis.  ...  ALB performed the analyses and drafted the manuscript. MPC assisted with revising the manuscript and formatting it for publication. Both authors read and approved the final manuscript.  ... 
doi:10.1186/1471-2105-13-92 pmid:22574964 pmcid:PMC3428669 fatcat:6jd5visy4nclpmrm6afetxp5oa

Integrating Microbiome Network: Establishing Linkages Between Plants, Microbes and Human Health

Suresh B. N. Krishna, Anamika Dubey, Muneer A. Malla, Richa Kothari, Chandrama P. Upadhyay, Jamila K. Adam, Ashwani Kumar
2019 Open Microbiology Journal  
Amidst the advancements in sequencing technologies, significant progress has been made to taxonomically and functionally catalogue these microbes and also to establish their exact role in the health and  ...  The trillions of microbes that colonize and live around us govern the health of both plants and animals through a cascade of direct and indirect mechanisms.  ...  Anamika Dubey would like to thank DST for financial supports in the form of DST inspire research Fellowship.  ... 
doi:10.2174/1874285801913020330 fatcat:bc76mjzi3jfptpnfjdqvbzbzpi

Functional assignment of metagenomic data: challenges and applications

T. Prakash, T. D. Taylor
2012 Briefings in Bioinformatics  
The level of confidence for functional predictions increases with increasing read-length.  ...  Functional analysis of the metagenomic data plays a central role in projects aiming to explore the most essential questions in microbiology, namely 'In a given environment, among the microbes present,  ...  APPLICATIONS OF METAGENOMIC FUNCTIONAL ANALYSIS Despite the challenges for metagenomic functional analysis, many studies exploring different environments Figure 4 : Status of functional prediction for  ... 
doi:10.1093/bib/bbs033 pmid:22772835 pmcid:PMC3504928 fatcat:ngqt43hyrbbllfl3uezaoxzk74

Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism

Jonathan Kennedy, Burkhardt Flemer, Stephen A. Jackson, David P. H. Lejon, John P. Morrissey, Fergal O'Gara, Alan D. W. Dobson
2010 Marine Drugs  
The presence of so many new gene families from these uncultured and highly diverse microbial populations represents a challenge for the understanding of and exploitation of the biology and biochemistry  ...  The application of new metagenomic and single cell genomics tools offers new ways to explore the complete metabolic diversity of the marine biome.  ...  WebCARMA hosted at http://webcarma.cebitec.uni-bielefeld.de has recently been developed to facilitate the functional and taxonomic classification of unassembled metagenomic reads as short as 35 bp [40  ... 
doi:10.3390/md8030608 pmid:20411118 pmcid:PMC2857354 fatcat:gsoiwsngz5hzjkzotc4dgnoqhe

A Mini Review on Metagenomics and its Implications in Ecological and Environmental Biotechnology

Patake, Patake
2011 unpublished
Its potential applications in in-situ restoration of ecosystems, designing strategies for bioremediation and in monitoring biodetereoration have come to the edge.  ...  In this review, we have reviewed current developments in metagenomics methodology with respect to applications in the field of Ecological Biotechnology and Environmental Biotechnologies.  ...  of ESTs and variable length prokaryotic genome sequence reads on related templet genomes Liang et al., 2009 WebCARMA http://webcarma.cebitec.unibilefeld.de A web application for the functional  ... 
fatcat:xw7bfvj3f5bnxm5325qrepvjvu
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