ArticleNucleic acids research2003
Protein families and TRIBES in genome sequence space.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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67 citing papers in PubMed, 131 citations in OpenAlex.
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- zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters.bioRxiv : the preprint server for biology · 2024Article
- CGG toolkit: Software components for computational genomics.PLoS computational biology · 2023Article
- MolluscDB: a genome and transcriptome database for molluscs.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2021Article
- Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study.Genome biology and evolution · 2020Article
- Extensive chromosomal rearrangements and rapid evolution of novel effector superfamilies contribute to host adaptation and speciation in the basal ascomycetous fungi.Molecular plant pathology · 2020Article
- No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects.Microbial biotechnology · 2018Review
- The scale-free nature of protein sequence space.PloS one · 2018Article
- KinFin: Software for Taxon-Aware Analysis of Clustered Protein Sequences.G3 (Bethesda, Md.) · 2017Article
- Percolation in protein sequence space.PloS one · 2017Article
- Trichinella spiralis: Adaptation and parasitism.Veterinary parasitology · 2016Article
- Gene-Family Extension Measures and Correlations.Life (Basel, Switzerland) · 2016Article
- Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus.Genome research · 2016Article
- Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution.Trends in microbiology · 2016Review
- On the origin of protein superfamilies and superfolds.Scientific reports · 2015Article
- Massive fungal biodiversity data re-annotation with multi-level clustering.Scientific reports · 2014Article
- A pluralistic account of homology: adapting the models to the data.Molecular biology and evolution · 2014Review
- Genome-wide transcriptional profiling of Botrytis cinerea genes targeting plant cell walls during infections of different hosts.Frontiers in plant science · 2014Article
- Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments.Molecular & cellular proteomics : MCP · 2013Review
- Meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling.Evolutionary bioinformatics online · 2012Article
7 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate detection of protein families allows assignment of protein function and the analysis of functional diversity in complete genomes. Recently, we presented a novel algorithm called TribeMCL for the detection of protein families that is both accurate and efficient. This method allows family analysis to be carried out on a very large scale. Using TribeMCL, we have generated a resource called TRIBES that contains protein family information, comprising annotations, protein sequence alignments and phylogenetic distributions describing 311 257 proteins from 83 completely sequenced genomes. The analysis of at least 60 934 detected protein families reveals that, with the essential families excluded, paralogy levels are similar between prokaryotes, irrespective of genome size. The number of essential families is estimated to be between 366 and 426. We also show that the currently known space of protein families is scale free and discuss the implications of this distribution. In addition, we show that smaller families are often formed by shorter proteins and discuss the reasons for this intriguing pattern. Finally, we analyse the functional diversity of protein families in entire genome sequences. The TRIBES protein family resource is accessible at http://www.ebi.ac.uk/research/cgg/tribes/.
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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.