ArticleF1000Research2016
Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.
Article in F1000Research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
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- Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential.BMC genomics · 2021Article
- A metabolic and physiological design study of Pseudomonas putida KT2440 capable of anaerobic respiration.BMC microbiology · 2021Article
- Effect of Sulfate on Carbon Monoxide Conversion by a Thermophilic Syngas-Fermenting Culture Dominated by aFrontiers in microbiology · 2020Article
- The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation.Scientific data · 2019Article
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- SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles.Bioinformatics (Oxford, England) · 2018Article
- Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio.Genome biology and evolution · 2018Article
- Complete Genome Sequence ofGenome announcements · 2017Article
- Metabolic modeling of energy balances in Mycoplasma hyopneumoniae shows that pyruvate addition increases growth rate.Biotechnology and bioengineering · 2017Article
- Draft Genome Sequence ofGenome announcements · 2017Article
- Concurrent Haloalkanoate Degradation and Chlorate Reduction by Pseudomonas chloritidismutans AW-1Applied and environmental microbiology · 2017Article
- Persistence of Functional Protein Domains in Mycoplasma Species and their Role in Host Specificity and Synthetic Minimal Life.Frontiers in cellular and infection microbiology · 2017Article
- Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells.Frontiers in microbiology · 2017Article
- Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data.Scientific reports · 2016Article
- Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.F1000Research · 2016Article
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5 authors.
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Abstract
A functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. Detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. We investigated the use of protein domain architectures for large scale functional comparative analysis as an alternative method. The performance of both approaches was assessed through functional comparison of 446 bacterial genomes sampled at different taxonomic levels. We show that protein domain architectures provide a fast and efficient alternative to methods based on sequence similarity to identify groups of functionally equivalent proteins within and across taxonomic boundaries, and it is suitable for large scale comparative analysis. Running both methods in parallel pinpoints potential functional adaptations that may add to bacterial fitness.
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