Classification of Long Noncoding RNAs by k-mer Content

• Published in: Methods in molecular biology Vol. 2254; p. 41
• Main Authors: Kirk, Jessime M, Sprague, Daniel, Calabrese, J Mauro
• Format: Journal Article
• Language: English
• Published: United States 2021
• Subjects: Algorithms; Cluster Analysis; Computational Biology - methods; Nucleotide Motifs - genetics; Protein Binding; RNA, Long Noncoding - classification; RNA, Long Noncoding - genetics; Networks; k-mer; Louvain algorithm; Communities; Sequence alignment; LncRNA; Protein-binding motif; Domain; Long noncoding RNA; Unsupervised clustering
• ISSN: 1064-3745; 1940-6029; 1940-6029
• DOI: 10.1007/978-1-0716-1158-6_4

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.