Novel read density distribution score shows possible aligner artefacts, when mapping a single chromosome.

Background: The use of artificial data to evaluate the performance of aligners and peak callers not only improves its accuracy and reliability, but also makes it possible to reduce the computational time. One of the natural ways to achieve such time reduction is by mapping a single chromosome.

Results: We investigated whether a single chromosome mapping causes any artefacts in the alignments' performances.

Statistical measures of the structure of genomic sequences: entropy, complexity, and position information.

Identifying regions of DNA with extreme statistical characteristics is an important aspect of the structural analysis of complete genomes. Linguistic methods, mainly based on estimating word frequency, can be used for this as they allow for the delineation of regions of low complexity. Low complexity may be due to biased nucleotide composition, by tandem- or dispersed repeats, by palindrome-hairpin structures, as well as by a combination of all these features.