Genome-Wide Tool for Sensitive de novo Identification and Visualisation of Interspersed and Tandem Repeats
Genomic repeats are functionally ubiquitous structural units found in all genomes. Studying these repeats of different origins is essential for understanding the evolution and adaptation of a given organism. These repeating patterns have manifold signatures and structures with varying degrees of hom...
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2024-12-01
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| Series: | Bioinformatics and Biology Insights |
| Online Access: | https://doi.org/10.1177/11779322241306391 |
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| author | Ruslan Kalendar Ulykbek Kairov |
| author_facet | Ruslan Kalendar Ulykbek Kairov |
| author_sort | Ruslan Kalendar |
| collection | DOAJ |
| description | Genomic repeats are functionally ubiquitous structural units found in all genomes. Studying these repeats of different origins is essential for understanding the evolution and adaptation of a given organism. These repeating patterns have manifold signatures and structures with varying degrees of homology, making their identification challenging. To address this challenge, we developed a new algorithm and software that can rapidly and accurately detect any repeated sequences de novo with varying degrees of homology in genomic sequences in interspersed or clustered repeats. Numerous forms of repeated sequences and complex patterns can be identified, even for complex sequence variants and implicit or mixed types of repeat blocks. Direct and inverted-repeat elements, perfect and imperfect microsatellite repeats, and any short or long tandem repeat belonging to a wide range of higher-order repeat structures of telomeres or large satellite sequences can be detected. By combining precision and versatility, our tool contributes significantly to elucidating the intricate landscape of genomic repeats. |
| format | Article |
| id | doaj-art-8dcc723d9af149bca4cd80a99ea7afa4 |
| institution | OA Journals |
| issn | 1177-9322 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Bioinformatics and Biology Insights |
| spelling | doaj-art-8dcc723d9af149bca4cd80a99ea7afa42025-08-20T01:58:41ZengSAGE PublishingBioinformatics and Biology Insights1177-93222024-12-011810.1177/11779322241306391Genome-Wide Tool for Sensitive de novo Identification and Visualisation of Interspersed and Tandem RepeatsRuslan Kalendar0Ulykbek Kairov1Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, KazakhstanLaboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, KazakhstanGenomic repeats are functionally ubiquitous structural units found in all genomes. Studying these repeats of different origins is essential for understanding the evolution and adaptation of a given organism. These repeating patterns have manifold signatures and structures with varying degrees of homology, making their identification challenging. To address this challenge, we developed a new algorithm and software that can rapidly and accurately detect any repeated sequences de novo with varying degrees of homology in genomic sequences in interspersed or clustered repeats. Numerous forms of repeated sequences and complex patterns can be identified, even for complex sequence variants and implicit or mixed types of repeat blocks. Direct and inverted-repeat elements, perfect and imperfect microsatellite repeats, and any short or long tandem repeat belonging to a wide range of higher-order repeat structures of telomeres or large satellite sequences can be detected. By combining precision and versatility, our tool contributes significantly to elucidating the intricate landscape of genomic repeats.https://doi.org/10.1177/11779322241306391 |
| spellingShingle | Ruslan Kalendar Ulykbek Kairov Genome-Wide Tool for Sensitive de novo Identification and Visualisation of Interspersed and Tandem Repeats Bioinformatics and Biology Insights |
| title | Genome-Wide Tool for Sensitive de novo Identification and Visualisation of Interspersed and Tandem Repeats |
| title_full | Genome-Wide Tool for Sensitive de novo Identification and Visualisation of Interspersed and Tandem Repeats |
| title_fullStr | Genome-Wide Tool for Sensitive de novo Identification and Visualisation of Interspersed and Tandem Repeats |
| title_full_unstemmed | Genome-Wide Tool for Sensitive de novo Identification and Visualisation of Interspersed and Tandem Repeats |
| title_short | Genome-Wide Tool for Sensitive de novo Identification and Visualisation of Interspersed and Tandem Repeats |
| title_sort | genome wide tool for sensitive de novo identification and visualisation of interspersed and tandem repeats |
| url | https://doi.org/10.1177/11779322241306391 |
| work_keys_str_mv | AT ruslankalendar genomewidetoolforsensitivedenovoidentificationandvisualisationofinterspersedandtandemrepeats AT ulykbekkairov genomewidetoolforsensitivedenovoidentificationandvisualisationofinterspersedandtandemrepeats |