| URL: | http://victoria.biengi.ac.ru/capsicum_tr/ |
| Full name: | Database of Capsicum annuum tandem repeats |
| Description: | The TRs detected in the C. annuum genome are placed into a database, which provides the following information for each TR-containing region: chromosome number, repeat length n_max, Z(n_max), coordinates in the chromosome, sequence, matrix Q_n^max and local alignment of the matrix. |
| Year founded: | 2023 |
| Last update: | 2023-04-25 |
| Version: | |
| Accessibility: |
Accessible
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| Country/Region: | Russian Federation |
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| University/Institution: | Institute of Bioengineering, Russian Academy of Sciences |
| Address: | Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow. |
| City: | Moscow |
| Province/State: | |
| Country/Region: | Russian Federation |
| Contact name (PI/Team): | Valentina Rudenko |
| Contact email (PI/Helpdesk): | v.m.rudenko@gmail.com |
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Detection of tandem repeats in the Capsicum annuum genome. [PMID: 37186267]
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. |