Multiple comparative metagenomics using multisetk-mer counting
نویسندگان
چکیده
منابع مشابه
Multiple comparative metagenomics using multiset k-mer counting
Background. Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or functional assignation rely on a small subset of the sequences that can be associated to known organisms. On the other hand, de novo methods, that compare the w...
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String Kernel (SK) techniques, especially those using gapped k-mers as features (gk), have obtained great success in classifying sequences like DNA, protein, and text. However, the state-of-the-art gk-SK runs extremely slow when we increase the dictionary size (Σ) or allow more mismatches (M). This is because current gk-SK uses a trie-based algorithm to calculate cooccurrence of mismatched subs...
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[1] Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud university medical centre, Nijmegen, The Netherlands. [2] Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil. [3] Computational Science Research Center, [4] Department of Mathematics, and [5] Department of Biology, San Diego St...
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The species complexity of microbial communities and challenges in culturing representative isolates make it difficult to obtain assembled genomes. Here we characterize and compare the metabolic capabilities of terrestrial and marine microbial communities using largely unassembled sequence data obtained by shotgun sequencing DNA isolated from the various environments. Quantitative gene content a...
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MOTIVATION Although many tools are available to study variation and its impact in single genomes, there is a lack of algorithms for finding such variation in metagenomes. This hampers the interpretation of metagenomics sequencing datasets, which are increasingly acquired in research on the (human) microbiome, in environmental studies and in the study of processes in the production of foods and ...
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ژورنال
عنوان ژورنال: PeerJ Computer Science
سال: 2016
ISSN: 2376-5992
DOI: 10.7717/peerj-cs.94