Sensitive protein alignments at tree-of-life scale using DIAMOND
By Benjamin Buchfink, Klaus Reuter, Hajk-Georg Drost. Nature Methods, 2021
4,034 citations recorded by the source corpus.
We are at the beginning of a genomic revolution in which all known species are planned to be sequenced. Accessing such data for comparative analyses is crucial in this new age of data-driven biology. Here, we introduce an improved version of DIAMOND 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. An updated version of DIAMOND uses improved algorithmic procedures and a customized high-performance computing framework to make seemingly prohibitive large-scale protein sequence alignments feasible.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/249e1dee04a6b52aefbc6136c3ef38e464005332
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In Molecular Biology
- Peer Bork
- Johannes Söding
- C. von Mering
- Martin Steinegger
- Lars Juhl Jensen
- Damian Szklarczyk
- Milot Mirdita
- Jillian F. Banfield
Citations in the corpus
- The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest (2022, methodology): “After the proteome is uploaded, STRING directly aligns the sequences to all sequences in its database using DIAMOND (58) (with the –iterate option).”
- Fast and accurate protein structure search with Foldseek (2022, methodology): “The most widely used approach to protein annotation and analysis is based on sequence similarity search 5–8 .”
- Petabase-scale sequence alignment catalyses viral discovery (2020, methodology): “DIAMOND output files (we label .pro) were specified with the command -f 6 qseqid qstart qend qlen qstrand sseqid sstart send slen pident evalue cigar qseq_translated full_qseq full_qseq_mate. coronaSPAdes.”
- Ensembl 2022 (2021, positive): “The comparison, based on Diamond (8), identifies the reciprocal best hits or the best hit (when no reciprocal best hit is available) to each representative genome to infer the closest homologue.”