ArticleBioinformatics (Oxford, England)2016
A multi-objective optimization approach accurately resolves protein domain architectures.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
- Pangenomic and functional domain comparison of enterotoxigenic Escherichia coli isolated from humans and swine: insights into host specificity.Molecular genetics and genomics : MGG · 2026Article
- Scaling the profile of life by function with SPIN.Bioinformatics advances · 2026Article
- Fidelity, specialization, and evolution of Paramecium PolX DNA polymerases involved in programmed double-strand break DNA repair.Nucleic acids research · 2025Article
- Creating and leveraging bespoke large-scale knowledge graphs for comparative genomics and multi-omics drug discovery with SocialGene.bioRxiv : the preprint server for biology · 2024Article
- Conserved and lineage-specific hypothetical proteins may have played a central role in the rise and diversification of major archaeal groups.BMC biology · 2022Article
- MyCLADE: a multi-source domain annotation server for sequence functional exploration.Nucleic acids research · 2021Article
- Protein domain identification methods and online resources.Computational and structural biotechnology journal · 2021Review
- Protein Family Content Uncovers Lineage Relationships and Bacterial Pathway Maintenance Mechanisms in DPANN Archaea.Frontiers in microbiology · 2021Article
- Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia and some have a novel nitrogenase paralog.The ISME journal · 2020Article
- Genomic Signature of Shifts in Selection in a Subalpine Ant and Its Physiological Adaptations.Molecular biology and evolution · 2020Article
- Article
- The distinction of CPR bacteria from other bacteria based on protein family content.Nature communications · 2019Article
- A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling.Microbiome · 2018Article
- Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms.Scientific reports · 2018Article
- Improving pairwise comparison of protein sequences with domain co-occurrence.PLoS computational biology · 2018Article
- Homology Inference Based on a Reconciliation Approach for the Comparative Genomics of Protozoa.Evolutionary bioinformatics online · 2018Article
- Domain prediction with probabilistic directional context.Bioinformatics (Oxford, England) · 2017Article
- Plasmobase: a comparative database of predicted domain architectures for Plasmodium genomes.Malaria journal · 2017Article
- Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence.PLoS computational biology · 2016Article
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4 authors.
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Abstract
motivationGiven a protein sequence and a number of potential domains matching it, what are the domain content and the most likely domain architecture for the sequence? This problem is of fundamental importance in protein annotation, constituting one of the main steps of all predictive annotation strategies. On the other hand, when potential domains are several and in conflict because of overlapping domain boundaries, finding a solution for the problem might become difficult. An accurate prediction of the domain architecture of a multi-domain protein provides important information for function prediction, comparative genomics and molecular evolution.
resultsWe developed DAMA (Domain Annotation by a Multi-objective Approach), a novel approach that identifies architectures through a multi-objective optimization algorithm combining scores of domain matches, previously observed multi-domain co-occurrence and domain overlapping. DAMA has been validated on a known benchmark dataset based on CATH structural domain assignments and on the set of Plasmodium falciparum proteins. When compared with existing tools on both datasets, it outperforms all of them. AVAILABILITY AND IMPLEMENTATION: DAMA software is implemented in C++ and the source code can be found at http://www.lcqb.upmc.fr/DAMA. CONTACT: juliana.silva_bernardes@upmc.fr or alessandra.carbone@lip6.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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