ArticleViruses2023
Rational Design of Profile HMMs for Sensitive and Specific Sequence Detection with Case Studies Applied to Viruses, Bacteriophages, and Casposons.
Article in Viruses, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 citing papers in PubMed, 3 citations in OpenAlex.
- RdDM-Associated Chromatin Remodelers in Soybean: Evolution and Stress-Induced Expression of CLASSY Genes.Plants (Basel, Switzerland) · 2025Article
- Integrating Sequence- and Structure-Based Similarity Metrics for the Demarcation of Multiple Viral Taxonomic Levels.Viruses · 2025Article
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4 authors at 3 institutions in 5 countries.
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Abstract
Profile hidden Markov models (HMMs) are a powerful way of modeling biological sequence diversity and constitute a very sensitive approach to detecting divergent sequences. Here, we report the development of protocols for the rational design of profile HMMs. These methods were implemented on TABAJARA, a program that can be used to either detect all biological sequences of a group or discriminate specific groups of sequences. By calculating position-specific information scores along a multiple sequence alignment, TABAJARA automatically identifies the most informative sequence motifs and uses them to construct profile HMMs. As a proof-of-principle, we applied TABAJARA to generate profile HMMs for the detection and classification of two viral groups presenting different evolutionary rates: bacteriophages of the
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