Tag: functional metagenomics

Some interesting new papers on functional analysius of metagenomics

By Jonathan Eisen   Posted in Scholarly Literature (Journals, Books, Reports)
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Some new papers that may be of interest to people: FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus. Statistical Methods for Functional Metagenomic Analysis Based on Next-Generation Sequencing Data PhD thesis from Pookhao, Naruekamol Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data Parallel-META 2.0: Enhanced …

Estimating average genome size from metagenomes

By Stephen Nayfach   Posted in Scholarly Literature (Journals, Books, Reports)
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We recently submitted a paper to biorxiv on the estimation of average genome size from shotgun metagenomics data and it’s application to the human microbiome (http://biorxiv.org/content/biorxiv/early/2014/09/11/009001.full.pdf). It is currently undergoing peer review. This study was motivated by the troubling observation that many universal single-copy genes appear to vary significantly across metagenomes. How can this be? …