Sensitive protein alignments at tree-of-life scale using DIAMOND
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Summary
An improved version of DIAMOND is introduced that greatly exceeds previous search performances and harnesses supercomputing to perform tree-of-life scale protein alignments in hours, while matching the sensitivity of the gold standard BLASTP.
- Type
- article
- Published
- 2021-04-01
- Cited by
- 4,256
- References
- 32
- Access
- Open access
- OpenAlex
- https://openalex.org/W3143063265
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:233185406
Keywords
Tree of life (biology), Diamond, Tree (set theory), Computer science, Matching (statistics)
References
- The design, implementation, and evaluation of mpiBLAST
- Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation
- How old is my gene?
- Fast and sensitive protein alignment using DIAMOND
- Protein database searches using compositionally adjusted substitution matrices
- Statistics of Local Complexity in Amino Acid Sequences and Sequence Databases
- UniRef: comprehensive and non-redundant UniProt reference clusters
- Identification of common molecular subsequences.
- A new repeat-masking method enables specific detection of homologous sequences
- SpEED: fast computation of sensitive spaced seeds
- Phylogenetic analysis of gene expression.
- Sort vs. Hash Revisited: Fast Join Implementation on Modern Multi-Core CPUs
- PatternHunter: faster and more sensitive homology search
- An evolutionarily structured universe of protein architecture.
- Striped Smith-Waterman speeds database searches six times over other SIMD implementations
- Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships.
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
- Kraken: ultrafast metagenomic sequence classification using exact alignments
- SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures
- Adaptive seeds tame genomic sequence comparison.
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- Simultaneous Single-Cell Genome and Transcriptome Sequencing of Termite Hindgut Protists Reveals Metabolic and Evolutionary Traits of Their Endosymbionts
- The National Ecological Observatory Network’s soil metagenomes: assembly and basic analysis
- WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
- Full-length sequencing of Ginkgo biloba L. reveals the synthesis of terpenoids during seed development
- Transcriptome Reveals Roles of Lignin-Modifying Enzymes and Abscisic Acid in the Symbiosis of Mycena and Gastrodia elata
- Gluconobacter oxydans Knockout Collection Finds Improved Rare Earth Element Extraction
- Proteo-Trancriptomic Analyses Reveal a Large Expansion of Metalloprotease-Like Proteins in Atypical Venom Vesicles of the Wasp Meteorus pulchricornis (Braconidae)
- SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs
- Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis
- Dynamic surveillance of mosquitoes and their viromes in Wuhan during 2020
- cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters
- proovframe: frameshift-correction for long-read (meta)genomics
- Unveiling the Gut Microbiota and Resistome of Wild Cotton Mice, Peromyscus gossypinus, from Heavy Metal- and Radionuclide-Contaminated Sites in the Southeastern United States
- Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes
- Chromosome-scale assembly of the yellow mealworm genome
- A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus)
- No Exchange of Picornaviruses in Vietnam between Humans and Animals in a High-Risk Cohort with Close Contact despite High Prevalence and Diversity
- Pathogenicity effector candidates and accessory genome revealed by pan-genomic analysis of Parastagonospora nodorum
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