Search for Highly Divergent Tandem Repeats in Amino Acid Sequences

Rudenko, V. М.; Korotkov, Eugene V.

doi:10.3390/ijms22137096

Cited by 2 publications

(3 citation statements)

References 45 publications

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“…4 ); the existence of lengthy TRs may be associated with chromatin compaction. It has been reported that in proteins, the most frequently observed repeat lengths are 2 and 7 amino acids, 41 which correspond to 6 and 21 bp, respectively.…”

Section: Resultsmentioning

confidence: 99%

“… 22–25 , 29 , 49 Some of them perform best in finding short perfect repeats, whereas the others are focused on weakly similar TRs with a relatively long period. 41 Comparison with the other methods such as TRF, 22 T-REKS, 24 and XSTREAM 25 could be useful for assessing the performance of mRPWM. However, different methods use various input parameters, which could affect the number of detected TRs 50 ; therefore, it is necessary to apply a common criterion of TR recognition for objective comparison.…”

Section: Discussionmentioning

confidence: 99%

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Detection of tandem repeats in the Capsicum annuum genome

Rudenko

Korotkov

2023

DNA Research

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Detection of tandem repeats in the Capsicum annuum genome

Rudenko

Korotkov

2023

DNA Research

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“…The MAHDS method was developed early for the multi alignment of promoter sequences and DNA sequences with weak similarity [ 18 , 19 , 20 ]. This method uses mathematical approaches and programs that were previously created to search for tandem repeats in various sequences [ 33 , 45 , 46 , 47 , 48 , 49 ]. In the present work, the site (3 June 2020) was used to construct a multiple alignment by the MAHDS method for various amino acid sequences.…”

Section: Methodsmentioning

confidence: 99%

Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences

Korotkov

Kostenko

2022

IJMS

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The aim of this work was to compare the multiple alignment methods MAHDS, T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK in their ability to align highly divergent amino acid sequences. To accomplish this, we created test amino acid sequences with an average number of substitutions per amino acid (x) from 0.6 to 5.6, a total of 81 sets. Comparison of the performance of sequence alignments constructed by MAHDS and previously developed algorithms using the CS and Z score criteria and the benchmark alignment database (BAliBASE) indicated that, although the quality of the alignments built with MAHDS was somewhat lower than that of the other algorithms, it was compensated by greater statistical significance. MAHDS could construct statistically significant alignments of artificial sequences with x ≤ 4.8, whereas the other algorithms (T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK) could not perform that at x > 2.4. The application of MAHDS to align 21 families of highly diverged proteins (identity < 20%) from Pfam and HOMSTRAD databases showed that it could calculate statistically significant alignments in cases when the other methods failed. Thus, MAHDS could be used to construct statistically significant multiple alignments of highly divergent protein sequences, which accumulated multiple mutations during evolution.

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Search for Highly Divergent Tandem Repeats in Amino Acid Sequences

Cited by 2 publications

References 45 publications

Detection of tandem repeats in the Capsicum annuum genome

Detection of tandem repeats in the Capsicum annuum genome

Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences

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