NDLI: Visual Analysis of the Quantitative Composition of Metagenomic Communities: the AmphoraVizu Webserver

Content Provider	Springer Nature Link
Author	Kerepesi, Csaba Szalkai, Balázs Grolmusz, Vince
Copyright Year	2014
Abstract	Low-cost DNA sequencing methods have given rise to an enormous development of metagenomics in the past few years. One basic— and difficult—task is the phylogenetic annotation of the metagenomic samples studied. The difficulty comes from the fact that the typical environmental sample contains hundreds of unknown and still uncharacterized microorganisms. There are several possible methods to assign at least partial phylogenetic information to these uncharacterized data. Originally, the 16S ribosomal RNA was used as phylogenetic marker, then genome sequence alignments and similarity measures between the unknown genome and the reference genomes were applied (e.g., in the MEGAN software), and more recently, phylogeny–based methods applying suitable sets of marker genes were suggested (AMPHORA, AMPHORA2, and the webserver implementation AmphoraNet). Here, we present a visual analysis tool that is capable of demonstrating the quantitative relations gained from the output of the AMPHORA2 program or the easy–to–use AmphoraNet webserver. Our web-based tool, the AmphoraVizu webserver, makes the phylogenetic distribution of the metagenomic sample clearly visible by using the native output format of AMPHORA2 or AmphoraNet. The user may set the phylogenetic resolution (i.e., superkingdom, phylum, class, order, family, genus, and species) along with the chart type and will receive the distribution data detailed for all relevant marker genes in the sample. For publication quality results, the chart labels can be customized by the user. The visualization webserver is available at the address http://amphoravizu.pitgroup.org . The AmphoraNet webserver is available at http://amphoranet.pitgroup.org . The open-source version of the AmphoraVizu program is available for download at http://pitgroup.org/apps/amphoravizu/AmphoraVizu.pl .
Starting Page	695
Ending Page	697
Page Count	3
File Format	PDF
ISSN	00953628
Journal	Microbial Ecology
Volume Number	69
Issue Number	3
e-ISSN	1432184X
Language	English
Publisher	Springer US
Publisher Date	2014-10-10
Publisher Place	Boston
Access Restriction	Subscribed
Subject Keyword	Quantitative metagenomic analysis Phylogenetics AmphoraNet AmphoraVizu Microbiology Ecology Microbial Ecology Geoecology/Natural Processes Nature Conservation Water Quality/Water Pollution
Content Type	Text
Resource Type	Article
Subject	Soil Science Ecology Ecology, Evolution, Behavior and Systematics

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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