Clustering huge protein sequence sets in linear time

Mutation effects predicted from sequence co-variation

(2017) Thomas A Hopf et al.   NATURE BIOTECHNOLOGY

Protein structure determination using metagenome sequence data

(2017) Sergey Ovchinnikov et al.   SCIENCE

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

(2016) Maria Hauser et al.   BIOINFORMATICS

Uniclust databases of clustered and deeply annotated protein sequences and alignments

(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

The MG-RAST metagenomics database and portal in 2015

(2015) Andreas Wilke et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

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

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

kClust: fast and sensitive clustering of large protein sequence databases

(2013) Maria Hauser et al.   BMC BIOINFORMATICS

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

IMG/M 4 version of the integrated metagenome comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications

(2013) Mengyao Zhao et al.   PLoS One

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Functional assignment of metagenomic data: challenges and applications

(2012) T. Prakash et al.   BRIEFINGS IN BIOINFORMATICS

Ultrafast clustering algorithms for metagenomic sequence analysis

(2012) W. Li et al.   BRIEFINGS IN BIOINFORMATICS

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

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

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

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS