ArticleGenome research2019
BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome.Nature biotechnology · 2026Article
- Genomic adaptations of novel halotolerant bacteria from extreme North Greenland.FEMS microbiology ecology · 2026Article
- DiscERN: an automated genome mining tool for the discovery of evolutionarily related natural products.Nature communications · 2026Article
- New genomic insights into long-chain alkenone biosynthesis by the coccolithophorid marine alga Gephyrocapsa huxleyi.BMC genomics · 2026Article
- Multi-Omic Assessment of Microbial Communities and Their Polyketide Biosynthetic Potential Across Abyssal Sediments.Environmental microbiology · 2026Article
- Genomic and chemical analyses of 713 marine biofilm-derived bacterial strains.Applied and environmental microbiology · 2026Article
- Recent strategies and methodological advances for microbial natural product research in the post-genomics era.Archives of microbiology · 2025Review
- Sequence modeling tools to decode the biosynthetic diversity of the human microbiome.mSystems · 2025Review
- Genomic Identification and Characterization of Saxitoxin Producing Cyanobacteria in Western Lake Erie Harmful Algal Blooms.Environmental science & technology · 2025Article
- Emergence and evolution of heterocyte glycolipid biosynthesis enabled specialized nitrogen fixation in cyanobacteria.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genome-resolved analysis of Serratia marcescens strain SMTT infers niche specialization as a hydrocarbon-degrader.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- HiFiBGC: an ensemble approach for improved biosynthetic gene cluster detection in PacBio HiFi-read metagenomes.BMC genomics · 2024Article
- Mining metagenomic data to gain a new insight into the gut microbial biosynthetic potential in placental mammals.Microbiology spectrum · 2024Article
- CLOCI: unveiling cryptic fungal gene clusters with generalized detection.Nucleic acids research · 2024Article
- Description of the complete rDNA repeat unit structure ofComparative cytogenetics · 2024Article
- Mitochondrial genome insights into the spatio-temporal distribution and genetic diversity ofFrontiers in plant science · 2024Article
- Does regulation hold the key to optimizing lipopeptide production inFrontiers in bioengineering and biotechnology · 2024Review
- Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes.Biomolecules · 2023Review
- Long-Read Metagenomics of Marine Microbes Reveals Diversely Expressed Secondary Metabolites.Microbiology spectrum · 2023Article
- Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Predicting biosynthetic gene clusters (BGCs) is critically important for discovery of antibiotics and other natural products. While BGC prediction from complete genomes is a well-studied problem, predicting BGCs in fragmented genomic assemblies remains challenging. The existing BGC prediction tools often assume that each BGC is encoded within a single contig in the genome assembly, a condition that is violated for most sequenced microbial genomes where BGCs are often scattered through several contigs, making it difficult to reconstruct them. The situation is even more severe in shotgun metagenomics, where the contigs are often short, and the existing tools fail to predict a large fraction of long BGCs. While it is difficult to assemble BGCs in a single contig, the structure of the genome assembly graph often provides clues on how to combine multiple contigs into segments encoding long BGCs. We describe biosyntheticSPAdes, a tool for predicting BGCs in assembly graphs and demonstrate that it greatly improves the reconstruction of BGCs from genomic and metagenomics data sets.
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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.