ArticleNucleic acids research2006
SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Pangenome Reveals Gene Content Variations and Structural Variants Contributing to Pig Characteristics.Genomics, proteomics & bioinformatics · 2025Article
- Whole-mitogenome analysis unveils previously undescribed genetic diversity in cane toads across their invasion trajectory.Ecology and evolution · 2024Article
- Discovery and Characterization of Linear Motif Mediated Protein-Protein Complexes.Advances in experimental medicine and biology · 2024Article
- The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology.GigaScience · 2023Article
- Computational Prediction of Protein Intrinsically Disordered Region Related Interactions and Functions.Genes · 2023Review
- The Australasian dingo archetype:bioRxiv : the preprint server for biology · 2023Article
- Modulating biomolecular condensates: a novel approach to drug discovery.Nature reviews. Drug discovery · 2022Review
- Transcript- and annotation-guided genome assembly of the European starling.Molecular ecology resources · 2022Article
- Intrinsically disordered proteins play diverse roles in cell signaling.Cell communication and signaling : CCS · 2022Review
- Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome.BMC genomics · 2021Article
- Resources to Discover and Use Short Linear Motifs in Viral Proteins.Trends in biotechnology · 2020Review
- IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions-Insights from transcription factors.Protein science : a publication of the Protein Society · 2020Article
- Intrinsically disordered domains: Sequence ➔ disorder ➔ function relationships.Protein science : a publication of the Protein Society · 2019Article
- Article
- Draft genome assembly of the invasive cane toad, Rhinella marina.GigaScience · 2018Article
- Mosquitoes as Suitable Vectors for Alphaviruses.Viruses · 2018Review
- Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins.Microbiome · 2017Article
- Predicting MoRFs in protein sequences using HMM profiles.BMC bioinformatics · 2016Article
- QSLiMFinder: improved short linear motif prediction using specific query protein data.Bioinformatics (Oxford, England) · 2015Article
- Computational identification of MoRFs in protein sequences.Bioinformatics (Oxford, England) · 2015Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many important interactions of proteins are facilitated by short, linear motifs (SLiMs) within a protein's primary sequence. Our aim was to establish robust methods for discovering putative functional motifs. The strongest evidence for such motifs is obtained when the same motifs occur in unrelated proteins, evolving by convergence. In practise, searches for such motifs are often swamped by motifs shared in related proteins that are identical by descent. Prediction of motifs among sets of biologically related proteins, including those both with and without detectable similarity, were made using the TEIRESIAS algorithm. The number of motif occurrences arising through common evolutionary descent were normalized based on treatment of BLAST local alignments. Motifs were ranked according to a score derived from the product of the normalized number of occurrences and the information content. The method was shown to significantly outperform methods that do not discount evolutionary relatedness, when applied to known SLiMs from a subset of the eukaryotic linear motif (ELM) database. An implementation of Multiple Spanning Tree weighting outperformed two other weighting schemes, in a variety of settings.
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