Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2009-09

AUTHORS

Arthur Brady, Steven L Salzberg

ABSTRACT

Metagenomics projects collect DNA from uncharacterized environments that may contain thousands of species per sample. One main challenge facing metagenomic analysis is phylogenetic classification of raw sequence reads into groups representing the same or similar taxa, a prerequisite for genome assembly and for analyzing the biological diversity of a sample. New sequencing technologies have made metagenomics easier, by making sequencing faster, and more difficult, by producing shorter reads than previous technologies. Classifying sequences from reads as short as 100 base pairs has until now been relatively inaccurate, requiring researchers to use older, long-read technologies. We present Phymm, a classifier for metagenomic data, that has been trained on 539 complete, curated genomes and can accurately classify reads as short as 100 base pairs, a substantial improvement over previous composition-based classification methods. We also describe how combining Phymm with sequence alignment algorithms improves accuracy. More... »

PAGES

673-676

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nmeth.1358

DOI

http://dx.doi.org/10.1038/nmeth.1358

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1008886215

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/19648916


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