Detection of tandem repeats in the Capsicum annuum genome

Abstract

In this study, we modified the multiple alignment method based on the generation of random position weight matrices (RPWM) and used it to search for tandem repeats (TRs) in the Capsicum annuum genome. The application of the modified (m)RPWM method, which considers the correlation of adjusting nucleotides, resulted in the identification of 908,072 TR regions with repeat lengths from 2 to 200 bp in the C. annuum genome, where they occupied ~29%. The most common TRs were 2 and 3 bp long followed by those of 21, 4, and 15 bp. We performed clustering analysis of TRs with repeat lengths of 2 and 21 bp and created position-weight matrices (PWMs) for each group; these templates could be used to search for TRs of a given length in any nucleotide sequence. All detected TRs can be accessed through publicly available database (http : //victoria.biengi.ac.ru/capsicum_tr/). Comparison of mRPWM with other TR search methods such as Tandem Repeat Finder, T-REKS, and XSTREAM indicated that mRPWM could detect significantly more TRs at similar false discovery rates, indicating its superior performance. The developed mRPWM method can be successfully applied to the identification of highly divergent TRs, which is important for functional analysis of genomes and evolutionary studies.

Study of Dispersed Repeats in the Cyanidioschyzon merolae Genome

“…The effectiveness of the IP method in finding weakly similar repeats that have accumulated a large number of mutations is due to the fact that instead of direct calculation of sequence alignment to determine similarity, this method constructs a PWM, which is an optimal image of multiple sequence alignment included in the family. The resulting PWMs function as templates to search for family members using dynamic programming and considering the correlation of neighboring bases [39]. Thus, the IP method can be applied to find repeats with a large number of indels, which are not recognized by k-mer-based methods; furthermore, the calculation of PWMs allows for building sequence consensuses for individual repeat families.…”