ArticleBioinformatics (Oxford, England)2016
A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes.
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 18 papers.
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18 citing papers in PubMed, 30 citations in OpenAlex.
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- Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation.PLoS genetics · 2020Article
- Genomic, transcriptomic, and proteomic insights into the symbiosis of deep-sea tubeworm holobionts.The ISME journal · 2020Article
- An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation.Nature communications · 2019Article
- Genome-Based Prediction of Bacterial Antibiotic Resistance.Journal of clinical microbiology · 2019Review
- Genomic correlates of extraintestinal infection are linked with changes in cell morphology in Campylobacter jejuni.Microbial genomics · 2019Article
- Evolution of Salmonella within Hosts.Trends in microbiology · 2018Review
- Population genomics of bacterial host adaptation.Nature reviews. Genetics · 2018Review
- Genome Variation and Molecular Epidemiology of Salmonella enterica Serovar Typhimurium Pathovariants.Infection and immunity · 2018Review
- Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica.PLoS genetics · 2018Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
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Abstract
motivationNext generation sequencing technologies have provided us with a wealth of information on genetic variation, but predicting the functional significance of this variation is a difficult task. While many comparative genomics studies have focused on gene flux and large scale changes, relatively little attention has been paid to quantifying the effects of single nucleotide polymorphisms and indels on protein function, particularly in bacterial genomics.
resultsWe present a hidden Markov model based approach we call delta-bitscore (DBS) for identifying orthologous proteins that have diverged at the amino acid sequence level in a way that is likely to impact biological function. We benchmark this approach with several widely used datasets and apply it to a proof-of-concept study of orthologous proteomes in an investigation of host adaptation in Salmonella enterica We highlight the value of the method in identifying functional divergence of genes, and suggest that this tool may be a better approach than the commonly used dN/dS metric for identifying functionally significant genetic changes occurring in recently diverged organisms. AVAILABILITY AND IMPLEMENTATION: A program implementing DBS for pairwise genome comparisons is freely available at: https://github.com/UCanCompBio/deltaBS CONTACT: nicole.wheeler@pg.canterbury.ac.nz or lars.barquist@uni-wuerzburg.deSupplementary information: Supplementary data are available at Bioinformatics online.
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