MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

MMseqs software suite for fast and deep clustering and searching of large protein sequence sets

(2016) Maria Hauser et al.   BIOINFORMATICS

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

(2015) Eric A. Franzosa et al.   NATURE REVIEWS MICROBIOLOGY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics

(2015) Ebrahim Afshinnekoo et al.   Cell Systems

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology

(2013) Bonnie L. Hurwitz et al.   PLoS One

From genomics to metagenomics

(2012) Narayan Desai et al.   CURRENT OPINION IN BIOTECHNOLOGY

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

(2011) Y. Zhao et al.   BIOINFORMATICS

Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

(2011) Torbjørn Rognes   BMC BIOINFORMATICS

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis

(2011) Matthew B. Scholz et al.   CURRENT OPINION IN BIOTECHNOLOGY

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

A new repeat-masking method enables specific detection of homologous sequences

(2010) Martin C. Frith   NUCLEIC ACIDS RESEARCH

The whole alignment and nothing but the alignment: the problem of spurious alignment flanks

(2008) Martin C. Frith et al.   NUCLEIC ACIDS RESEARCH