Beyond tandem repeats: complex pattern structures and distant regions of similarity

Abstract

We extend previous algorithmic research to a class of regular tandem repeats (RegTRs). We formally define RegTRs, as well as two important subclasses: VLTRs and MPTRs. We present algorithms for identification of TRs in these classes. Furthermore, our algorithms identify degenerate VLTRs and MPTRs: repeats containing substitutions, insertions and deletions. To illustrate our work, we present results of our analysis for two difficult regions in cattle and human data which reflect practical occurrences of these subclasses in GenBank sequence data. In addition, we show the applicability of our algorithmic techniques for identifying Alu sequences, gene clusters and other distant regions of similarity. We illustrate this with an example from yeast chromosome I.

Joint Use of Different Homogeneity Testing Criteria for Latent Periodicity Revelation in Biological Sequences

“…Для выявления периодичности в биологических строках ранее широко использовались методы Фурье-и вейвлет-анализа [17][18][19][20][21], комбинаторные методы и методы динамического программирования [1, 3,4,[22][23][24], различные статистические критерии проверки однородности строк [25][26][27][28][29] и др., см., например, обзор [30]. Однако по сравнению со статистическими критериями Фурье-анализ имеет плохую чувствительность к паттернам периодичности, размер которых в несколько раз превышает размер алфавита анализируемой строки [26].…”

Finding Approximate Tandem Repeats in Genomic Sequences

“…More widely applicable algorithms have been proposed in [6,37,39]. Other related algorithms are [26,18,35].…”

Techniques for detecting approximate tandem repeats in DNA

“…However, the evolutionary force criterion still does not define precisely what is meant by an ATR (note that property 2 is valid only in the first round of merging). In particular, this heuristic method is not as general as other ATR finding algorithms such as [12,13,14]. A more general approach to finding ATRs, or approximate periodicities, in DNA can be formulated by using the Fourier product method, described in the next section.…”

“…ATRs pose more of a challenge as substitutions, insertions, and deletions through millions of years of evolution make the repeats harder to detect. Recently algorithms have been proposed [12,13,14], each with its own limitations and assumptions. In [12], the period of the repeat is limited to less than 2000 base pairs (bp) as of version 3.21.…”

“…In [12], the period of the repeat is limited to less than 2000 base pairs (bp) as of version 3.21. In [14], there are practical memory constraints resulting from the pattern extension algorithm. Although there are no limitations on the period size in [13], the algorithm does not deal with insertions or deletions (indels) directly, and as such, certain repeats with indels can be missed.…”