Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

Martin Steinegger; Milot Mirdita; Johannes Söding

doi:10.1038/s41592-019-0437-4

Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

Nat Methods. 2019 Jul;16(7):603-606. doi: 10.1038/s41592-019-0437-4. Epub 2019 Jun 24.

Authors

Martin Steinegger^{1

2

3}, Milot Mirdita⁴, Johannes Söding⁵

Affiliations

¹ Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany. [email protected].
² Department of Chemistry, Seoul National University, Seoul, Korea. [email protected].
³ Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA. [email protected].
⁴ Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany.
⁵ Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany. [email protected].

PMID: 31235882
DOI: 10.1038/s41592-019-0437-4

Abstract

The open-source de novo protein-level assembler, Plass ( https://plass.mmseqs.com ), assembles six-frame-translated sequencing reads into protein sequences. It recovers 2-10 times more protein sequences from complex metagenomes and can assemble huge datasets. We assembled two redundancy-filtered reference protein catalogs, 2 billion sequences from 640 soil samples (soil reference protein catalog) and 292 million sequences from 775 marine eukaryotic metatranscriptomes (marine eukaryotic reference catalog), the largest free collections of protein sequences.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence
Codon
Metagenomics*
Open Reading Frames
Proteins / chemistry*

Substances

Codon
Proteins