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      Analysis of 16S rRNA environmental sequences using MEGAN

      research-article
      1 , , 1 , 1
      BMC Genomics
      BioMed Central
      Asia Pacific Bioinformatics Network (APBioNet) Tenth International Conference on Bioinformatics – First ISCB Asia Joint Conference 2011 (InCoB/ISCB-Asia 2011)
      30 November-2 December 2011

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          Abstract

          Background

          Metagenomics is a rapidly growing field of research aimed at studying assemblages of uncultured organisms using various sequencing technologies, with the hope of understanding the true diversity of microbes, their functions, cooperation and evolution. There are two main approaches to metagenomics: amplicon sequencing, which involves PCR-targeted sequencing of a specific locus, often 16S rRNA, and random shotgun sequencing. Several tools or packages have been developed for analyzing communities using 16S rRNA sequences. Similarly, a number of tools exist for analyzing randomly sequenced DNA reads.

          Results

          We describe an extension of the metagenome analysis tool MEGAN, which allows one to analyze 16S sequences. For the analysis all 16S sequences are blasted against the SILVA database. The result output is imported into MEGAN, using a synonym file that maps the SILVA accession numbers onto the NCBI taxonomy.

          Conclusions

          Environmental samples are often studied using both targeted 16S rRNA sequencing and random shotgun sequencing. Hence tools are needed that allow one to analyze both types of data together, and one such tool is MEGAN. The ideas presented in this paper are implemented in MEGAN 4, which is available from: http://www-ab.informatik.uni-tuebingen.de/software/megan.

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          Most cited references3

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          GenBank

          GenBank® is a comprehensive database that contains publicly available DNA sequences for more than 165 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in the UK and the DNA Data Bank of Japan helps to ensure worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at http://www.ncbi.nlm.nih.gov.
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            Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes.

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              MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

              Background Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem. Results Existing algorithms are largely optimized for speed and coverage; in contrast, we present here a software framework that focuses on a restricted set of informative gene families, using Maximum Likelihood to assign these with the best possible accuracy. This framework ('MLTreeMap'; http://mltreemap.org/) uses raw nucleotide sequences as input, and includes hand-curated, extensible reference information. Conclusions We discuss how we validated our pipeline using complete genomes as well as simulated and actual environmental sequences.
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                Author and article information

                Conference
                BMC Genomics
                BMC Genomics
                BMC Genomics
                BioMed Central
                1471-2164
                2011
                30 November 2011
                : 12
                : Suppl 3
                : S17
                Affiliations
                [1 ]Center for Bioinformatics ZBIT, Tübingen University, Sand 14, 72076 Tübingen, Germany
                Article
                1471-2164-12-S3-S17
                10.1186/1471-2164-12-S3-S17
                3333176
                22369513
                91ddc83f-0b28-4571-9bb7-50feb67ae6b8
                Copyright ©2011 Mitra et al; licensee BioMed Central Ltd.

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Asia Pacific Bioinformatics Network (APBioNet) Tenth International Conference on Bioinformatics – First ISCB Asia Joint Conference 2011 (InCoB/ISCB-Asia 2011)
                Kuala Lumpur, Malaysia
                30 November-2 December 2011
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                Genetics
                Genetics

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