ArticleMethods in molecular biology (Clifton, N.J.)2021
Classification of Long Noncoding RNAs by k-mer Content.
Article in Methods in molecular biology (Clifton, N.J.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 18 citations in OpenAlex.
- Scanning transcriptomes for nonlinear, domain-level similarities using hmSEEKR.bioRxiv : the preprint server for biology · 2026Article
- Improved functions for nonlinear sequence comparison using SEEKR.RNA (New York, N.Y.) · 2024Article
- Distribution rules of 8-mer spectra and characterization of evolution state in animal genome sequences.BMC genomics · 2024Article
- ASLncR: a novel computational tool for prediction of abiotic stress-responsive long non-coding RNAs in plants.Functional & integrative genomics · 2023Article
- NCodR: A multi-class support vector machine classification to distinguish non-coding RNAs in Viridiplantae.Quantitative plant biology · 2022Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
K-mer based comparisons have emerged as powerful complements to BLAST-like alignment algorithms, particularly when the sequences being compared lack direct evolutionary relationships. In this chapter, we describe methods to compare k-mer content between groups of long noncoding RNAs (lncRNAs), to identify communities of lncRNAs with related k-mer contents, to identify the enrichment of protein-binding motifs in lncRNAs, and to scan for domains of related k-mer contents in lncRNAs. Our step-by-step instructions are complemented by Python code deposited in Github. Though our chapter focuses on lncRNAs, the methods we describe could be applied to any set of nucleic acid sequences.
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Registered trials
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