Fast and sensitive protein alignment using DIAMOND

By Benjamin Buchfink, Chao Xie, Daniel H. Huson. 2014

11,765 citations recorded by the source corpus.

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In Molecular Biology

Citations in the corpus

HH-suite3 for fast remote homology detection and deep protein annotation (2019, methodology): “In recent years, various sequence search tools have been developed that are up to four orders of magnitude faster than BLAST [15–18].”
Clustering huge protein sequence sets in linear time (2017, background): “At 50% identity, Linclust clusters the 123 million sequences 10 times faster than Linclust/MMseqs2 and, by extrapolation, 2300 times faster than UCLUST, 720 times faster than MMseqs, 4600 times faster than CD-HIT, 1600 times faster than DIAMOND [12], 69 000 times faster than MASH [13], and 26 000 ti”
MMseqs2: sensitive protein sequence searching for the analysis of massive data sets (2017, methodology): “Many use spaced k-mer seeds to avoid strongly overlapping, multiple matches [4, 12].”
MGnify: the microbiome analysis resource in 2020 (2019, methodology): “Finally, the proteins are also compared individually against the UniRef90 (46) database using DIAMOND (47) in ‘blastP’ mode to identify the accession, description and taxonomic identifier of the best matching sequence.”
Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases (2019, neutral): “Our community is testing the ability to import preexisting BLAST or DIAMOND XML result files (Buchfink et al. 2015), and new manners of visualizing results (Wintersinger and Wasmuth 2015; Cui et al.”
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities (2018, methodology): “This file is used to align the input genome files given by the user (using DIAMOND (35)) and find the corresponding homologous genes in the BiGG database.”
Identifying viruses from metagenomic data using deep learning (2020, methodology): “Gene homology-based methods, VIROME [9], DIA-MOND [13], VirSorter [4], JGI Earth Virome Pipeline [19], MARVEL [6], and most provirus ﬁ nding tools, Prophinder [15], Phage-Finder [14], PhiSpy [16], and PHASTER [17], determine viral sequences mainly by comparing genes in the query sequence against…”
PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics (2017, methodology): “The replacement of NCBI BLAST was decided upon due to the massive computational performance gains introduced by the DIAMOND program, while maintaining sensitivity and specificity comparable to NCBI BLAST.”
A review of methods and databases for metagenomic classification and assembly (2019, methodology): “faster than BLASTX [70] https://github.”