Speeding up all-against-all protein comparisons while maintaining sensitivity by considering subsequence-level homology

Big data and other challenges in the quest for orthologs

(2014) E. L. L. Sonnhammer et al.   BIOINFORMATICS

kClust: fast and sensitive clustering of large protein sequence databases

(2013) Maria Hauser et al.   BMC BIOINFORMATICS

Hieranoid: Hierarchical Orthology Inference

(2013) Fabian Schreiber et al.   JOURNAL OF MOLECULAR BIOLOGY

Functional and evolutionary implications of gene orthology

(2013) Toni Gabaldón et al.   NATURE REVIEWS GENETICS

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs

(2013) Adrian M. Altenhoff et al.   PLoS One

Toward community standards in the quest for orthologs

(2012) C. Dessimoz et al.   BIOINFORMATICS

Roundup 2.0: enabling comparative genomics for over 1800 genomes

(2012) T. F. DeLuca et al.   BIOINFORMATICS

OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

(2012) Robert M. Waterhouse et al.   NUCLEIC ACIDS RESEARCH

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs

(2012) Adrian M. Altenhoff et al.   PLoS Computational Biology

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

(2011) P. Gaudet et al.   BRIEFINGS IN BIOINFORMATICS

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

(2011) I. Pagani et al.   NUCLEIC ACIDS 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

OMA 2011: orthology inference among 1000 complete genomes

(2010) A. M. Altenhoff et al.   NUCLEIC ACIDS RESEARCH

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Protein function prediction – the power of multiplicity

(2009) Robert Rentzsch et al.   TRENDS IN BIOTECHNOLOGY

Algorithm of OMA for large-scale orthology inference

(2008) Alexander CJ Roth et al.   BMC BIOINFORMATICS

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH