publication . Other literature type . Article . 2017 . Embargo end date: 14 Aug 2017

MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis

Christian von Mering; João F Matias Rodrigues;
Open Access
  • Published: 14 Aug 2017
  • Publisher: Oxford University Press
  • Country: Switzerland
Abstract
Abstract Motivation Ribosomal RNA profiling has become crucial to studying microbial communities, but meaningful taxonomic analysis and inter-comparison of such data are still hampered by technical limitations, between-study design variability and inconsistencies between taxonomies used. Results Here we present MAPseq, a framework for reference-based rRNA sequence analysis that is up to 30% more accurate (F½ score) and up to one hundred times faster than existing solutions, providing in a single run multiple taxonomy classifications and hierarchical operational taxonomic unit mappings, for rRNA sequences in both amplicon and shotgun sequencing strategies, and fo...
Subjects
free text keywords: Institute of Molecular Life Sciences, Systems Biology / Functional Genomics, From Genomes to Ecosystems [Evolution in Action], 570 Life sciences; biology, Statistics and Probability, Computational Theory and Mathematics, Biochemistry, Molecular Biology, Computational Mathematics, Computer Science Applications, Applications Notes, Sequence Analysis
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Abstract
Abstract Motivation Ribosomal RNA profiling has become crucial to studying microbial communities, but meaningful taxonomic analysis and inter-comparison of such data are still hampered by technical limitations, between-study design variability and inconsistencies between taxonomies used. Results Here we present MAPseq, a framework for reference-based rRNA sequence analysis that is up to 30% more accurate (F½ score) and up to one hundred times faster than existing solutions, providing in a single run multiple taxonomy classifications and hierarchical operational taxonomic unit mappings, for rRNA sequences in both amplicon and shotgun sequencing strategies, and fo...
Subjects
free text keywords: Institute of Molecular Life Sciences, Systems Biology / Functional Genomics, From Genomes to Ecosystems [Evolution in Action], 570 Life sciences; biology, Statistics and Probability, Computational Theory and Mathematics, Biochemistry, Molecular Biology, Computational Mathematics, Computer Science Applications, Applications Notes, Sequence Analysis
Related Organizations

Al-Ghalith G.A.et al (2016) NINJA-OPS: fast accurate marker gene alignment using concatenated ribosomes. PLoS Comput. Biol., 12, e1004658.26820746 [OpenAIRE] [PubMed]

Caporaso J.G.et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat. Methods, 7, 335–336.20383131 [OpenAIRE] [PubMed]

Edgar R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460–2461.20709691 [PubMed]

Rognes T.et al (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ, 4, e2584.27781170 [OpenAIRE] [PubMed]

Schloss P.D.et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol., 75, 7537–7541.19801464 [OpenAIRE] [PubMed]

Wang Q.et al (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol., 73, 5261–5267.17586664 [OpenAIRE] [PubMed]

Yilmaz P.et al (2014) The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Res., 42, D643–D648.24293649 [OpenAIRE] [PubMed]

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