ArticleBMC genomics2020
Progress in quickly finding orthologs as reciprocal best hits: comparing blast, last, diamond and MMseqs2.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
44 citing papers in PubMed.
- DetectNAR genomics and bioinformatics · 2026Article
- WASP: a pipeline for functional annotation prediction based on AlphaFold structural models.Nature communications · 2026Article
- A systems-level atlas of carbon-response transcriptional states inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Adaptations in electron transport chain complexes of clinical Rhodococcus equi revealed through comparative genomics.World journal of microbiology & biotechnology · 2026Article
- Hemoglobin Digestion Genes Are Conserved in Lizard-InfectiveEcology and evolution · 2026Article
- Article
- Identification and characteristics of a novel fosfomycin glutathione transferase, FosA12, from an MDR clinical isolate ofAntimicrobial agents and chemotherapy · 2026Article
- The evolution of the Vibrio genome: the discovery of the pan-genome and the functional specialization of chromosomes.Molecular genetics and genomics : MGG · 2026Article
- Genomic landscape and genetic manipulation of an ectoparasitoid wasp, Gregopimpla kuwanae.Communications biology · 2026Article
- Episodic positive selection structurally stabilizes the Arabidopsis CONSTANS-like gene COL5 indicating adaptive evolution.Scientific reports · 2026Article
- Exploring the molecular landscape of environmental responses in the Antarctic plantFrontiers in plant science · 2026Article
- Mitochondrial metabolic remodeling and multi-omics profiling identify plasma biomarkers of myocardial infarction.Journal of molecular and cellular cardiology plus · 2025Article
- Identification and classification of ion-channels across the tree of life provide functional insights into understudied CALHM channels.bioRxiv : the preprint server for biology · 2025Article
- Evaluating sequence and structural similarity metrics for predicting shared paralog functions.NAR genomics and bioinformatics · 2025Article
- Metatranscriptomic Analysis Uncovers RNA Virus Diversity in Ticks From the China-Russia-North Korea Border Region.Transboundary and emerging diseases · 2025Article
- Article
- MetaCompare 2.0: differential ranking of ecological and human health resistome risks.FEMS microbiology ecology · 2024Article
- Genetic potential for aerobic respiration and denitrification in globally distributed respiratory endosymbionts.Nature communications · 2024Article
- Metagenomic functional profiling: to sketch or not to sketch?Bioinformatics (Oxford, England) · 2024Article
- Decoding functional proteome information in model organisms using protein language models.NAR genomics and bioinformatics · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFinding orthologs remains an important bottleneck in comparative genomics analyses. While the authors of software for the quick comparison of protein sequences evaluate the speed of their software and compare their results against the most usual software for the task, it is not common for them to evaluate their software for more particular uses, such as finding orthologs as reciprocal best hits (RBH). Here we compared RBH results obtained using software that runs faster than blastp. Namely, lastal, diamond, and MMseqs2.
resultsWe found that lastal required the least time to produce results. However, it yielded fewer results than any other program when comparing the proteins encoded by evolutionarily distant genomes. The program producing the most similar number of RBH to blastp was diamond ran with the "ultra-sensitive" option. However, this option was diamond's slowest, with the "very-sensitive" option offering the best balance between speed and RBH results. The speeding up of the programs was much more evident when dealing with eukaryotic genomes, which code for more numerous proteins. For example, lastal took a median of approx. 1.5% of the blastp time to run with bacterial proteomes and 0.6% with eukaryotic ones, while diamond with the very-sensitive option took 7.4% and 5.2%, respectively. Though estimated error rates were very similar among the RBH obtained with all programs, RBH obtained with MMseqs2 had the lowest error rates among the programs tested.
conclusionsThe fast algorithms for pairwise protein comparison produced results very similar to blast in a fraction of the time, with diamond offering the best compromise in speed, sensitivity and quality, as long as a sensitivity option, other than the default, was chosen.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.