Lineage-associated underrepresented permutations (LAUPs) of mammalian genomic sequences based on a Jellyfish-based LAUPs analysis application (JBLA) | Zendy

Le Zhang | Zendy; Ming Xiao | Zendy; Jingsong Zhou | Zendy; Jun Yu | Zendy

Open Access

Lineage-associated underrepresented permutations (LAUPs) of mammalian genomic sequences based on a Jellyfish-based LAUPs analysis application (JBLA)

Author(s) -

Le Zhang,

Ming Xiao,

Jingsong Zhou,

Jun Yu

Publication year - 2018

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bty392

Subject(s) - jellyfish , cpg site , genome , biology , lineage (genetic) , evolutionary biology , sequence (biology) , genetics , gene , computational biology , genomics , human genome , dna methylation , gene expression , ecology

This study addresses several important questions related to naturally underrepresented sequences: (i) are there permutations of real genomic DNA sequences in a defined length (k-mer) and a given lineage that do not actually exist or underrepresented? (ii) If there are such sequences, what are their characteristics in terms of k-mer length and base composition? (iii) Are they related to CpG or TpA underrepresentation known for human sequences? We propose that the answers to these questions are of great significance for the study of sequence-associated regulatory mechanisms, such cytosine methylation and chromosomal structures in physiological or pathological conditions such as cancer.

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