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Updated: Jan 23, 2026

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
Published on: December 22, 2014
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold
Martin Steinegger1,2,3, Milot Mirdita4, Johannes Söding5
1Quantitative and Computational Biology Group, Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany. martin.steinegger@mpibpc.mpg.de.
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.
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