title: DNA word analysis based on the distribution of the distances between symmetric words.
abstract: We address the problem of discovering pairs of symmetric genomic words (i.e., words and the corresponding reversed complements) occurring at distances that are overrepresented. For this purpose, we developed new procedures to identify symmetric word pairs with uncommon empirical distance distribution and with clusters of overrepresented short distances. We speculate that patterns of overrepresentation of short distances between symmetric word pairs may allow the occurrence of non-standard DNA conformations, such as hairpin/cruciform structures. We focused on the human genome, and analysed both the complete genome as well as a version with known repetitive sequences masked out. We reported several well-defined features in the distributions of distances, which can be classified into three different profiles, showing enrichment in distinct distance ranges. We analysed in greater detail certain pairs of symmetric words of length seven, found by our procedure, characterised by the surprising fact that they occur at single distances more frequently than expected.
authors.affiliation: Department of Mathematics & CIDMA, University of Aveiro, Aveiro, Portugal.|Department of Medical Sciences & iBiMED, University of Aveiro, Aveiro, Portugal.
authors.forename: Ana H M P
authors.identifier: http://orcid.org/0000-0003-4632-3561
authors.initials: AHMP
authors.lastname: Tavares
authors.affiliation: Department of Electronics, Telecommunications and Informatics, University of Aveiro, Aveiro, Portugal.|IEETA, University of Aveiro, Aveiro, Portugal.
authors.forename: Armando J
authors.initials: AJ
authors.lastname: Pinho
authors.affiliation: Department of Medical Sciences & iBiMED, University of Aveiro, Aveiro, Portugal.|IEETA, University of Aveiro, Aveiro, Portugal.
authors.forename: Raquel M
authors.initials: RM
authors.lastname: Silva
authors.affiliation: Department of Electronics, Telecommunications and Informatics, University of Aveiro, Aveiro, Portugal.|IEETA, University of Aveiro, Aveiro, Portugal.
authors.forename: João M O S
authors.identifier: http://orcid.org/0000-0001-9187-8094
authors.initials: JMOS
authors.lastname: Rodrigues
authors.affiliation: Department of Electronics, Telecommunications and Informatics, University of Aveiro, Aveiro, Portugal.|IEETA, University of Aveiro, Aveiro, Portugal.
authors.forename: Carlos A C
authors.initials: CAC
authors.lastname: Bastos
authors.affiliation: Department of Electronics, Telecommunications and Informatics, University of Aveiro, Aveiro, Portugal.|IEETA, University of Aveiro, Aveiro, Portugal.
authors.forename: Paulo J S G
authors.initials: PJSG
authors.lastname: Ferreira
authors.affiliation: Department of Mathematics & CIDMA, University of Aveiro, Aveiro, Portugal. vera@ua.pt.|Department of Medical Sciences & iBiMED, University of Aveiro, Aveiro, Portugal. vera@ua.pt.|IEETA, University of Aveiro, Aveiro, Portugal. vera@ua.pt.
authors.forename: Vera
authors.identifier: http://orcid.org/0000-0003-1051-8084
authors.initials: V
authors.lastname: Afreixo
mesh_terms: D000465:Algorithms; D002877:Chromosomes, Human; D004247:DNA / Q000737:chemistry / Q000235:genetics; D030541:Databases, Genetic; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D006801:Humans; D008390:Markov Chains; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D017422:Sequence Analysis, DNA / Q000379:methods; D013329:Structure-Activity Relationship
chemical_list: D004247:DNA