ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation
Abstract Background Mitochondria is a powerhouse of all eukaryotic cells that have its own circular DNA (mtDNA) encoding various RNAs and proteins. Somatic perturbations of mtDNA are accumulating with age thus it is of great importance to uncover the main sources of mtDNA instability. Recent analyse...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-05-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-019-5536-1 |
| _version_ | 1830489254254346240 |
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| author | Viktor N. Shamanskiy Valeria N. Timonina Konstantin Yu. Popadin Konstantin V. Gunbin |
| author_facet | Viktor N. Shamanskiy Valeria N. Timonina Konstantin Yu. Popadin Konstantin V. Gunbin |
| author_sort | Viktor N. Shamanskiy |
| collection | DOAJ |
| description | Abstract Background Mitochondria is a powerhouse of all eukaryotic cells that have its own circular DNA (mtDNA) encoding various RNAs and proteins. Somatic perturbations of mtDNA are accumulating with age thus it is of great importance to uncover the main sources of mtDNA instability. Recent analyses demonstrated that somatic mtDNA deletions depend on imperfect repeats of various nature between distant mtDNA segments. However, till now there are no comprehensive databases annotating all types of imperfect repeats in numerous species with sequenced complete mitochondrial genome as well as there are no algorithms capable to call all types of imperfect repeats in circular mtDNA. Results We implemented naïve algorithm of pattern recognition by analogy to standard dot-plot construction procedures allowing us to find both perfect and imperfect repeats of four main types: direct, inverted, mirror and complementary. Our algorithm is adapted to specific characteristics of mtDNA such as circularity and an excess of short repeats - it calls imperfect repeats starting from the length of 10 b.p. We constructed interactive web available database ImtRDB depositing perfect and imperfect repeats positions in mtDNAs of more than 3500 Vertebrate species. Additional tools, such as visualization of repeats within a genome, comparison of repeat densities among different genomes and a possibility to download all results make this database useful for many biologists. Our first analyses of the database demonstrated that mtDNA imperfect repeats (i) are usually short; (ii) associated with unfolded DNA structures; (iii) four types of repeats positively correlate with each other forming two equivalent pairs: direct and mirror versus inverted and complementary, with identical nucleotide content and similar distribution between species; (iv) abundance of repeats is negatively associated with GC content; (v) dinucleotides GC versus CG are overrepresented on light chain of mtDNA covered by repeats. Conclusions ImtRDB is available at http://bioinfodbs.kantiana.ru/ImtRDB/. It is accompanied by the software calling all types of interspersed repeats with different level of degeneracy in circular DNA. This database and software can become a very useful tool in various areas of mitochondrial and chloroplast DNA research. |
| first_indexed | 2024-12-21T19:34:20Z |
| format | Article |
| id | doaj.art-493c27975c384549a794a74632e72a1c |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T19:34:20Z |
| publishDate | 2019-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-493c27975c384549a794a74632e72a1c2022-12-21T18:52:38ZengBMCBMC Genomics1471-21642019-05-0120S311710.1186/s12864-019-5536-1ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotationViktor N. Shamanskiy0Valeria N. Timonina1Konstantin Yu. Popadin2Konstantin V. Gunbin3Center for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal UniversityCenter for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal UniversityCenter for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal UniversityCenter for Mitochondrial Functional Genomics, School of Life Science, Immanuel Kant Baltic Federal UniversityAbstract Background Mitochondria is a powerhouse of all eukaryotic cells that have its own circular DNA (mtDNA) encoding various RNAs and proteins. Somatic perturbations of mtDNA are accumulating with age thus it is of great importance to uncover the main sources of mtDNA instability. Recent analyses demonstrated that somatic mtDNA deletions depend on imperfect repeats of various nature between distant mtDNA segments. However, till now there are no comprehensive databases annotating all types of imperfect repeats in numerous species with sequenced complete mitochondrial genome as well as there are no algorithms capable to call all types of imperfect repeats in circular mtDNA. Results We implemented naïve algorithm of pattern recognition by analogy to standard dot-plot construction procedures allowing us to find both perfect and imperfect repeats of four main types: direct, inverted, mirror and complementary. Our algorithm is adapted to specific characteristics of mtDNA such as circularity and an excess of short repeats - it calls imperfect repeats starting from the length of 10 b.p. We constructed interactive web available database ImtRDB depositing perfect and imperfect repeats positions in mtDNAs of more than 3500 Vertebrate species. Additional tools, such as visualization of repeats within a genome, comparison of repeat densities among different genomes and a possibility to download all results make this database useful for many biologists. Our first analyses of the database demonstrated that mtDNA imperfect repeats (i) are usually short; (ii) associated with unfolded DNA structures; (iii) four types of repeats positively correlate with each other forming two equivalent pairs: direct and mirror versus inverted and complementary, with identical nucleotide content and similar distribution between species; (iv) abundance of repeats is negatively associated with GC content; (v) dinucleotides GC versus CG are overrepresented on light chain of mtDNA covered by repeats. Conclusions ImtRDB is available at http://bioinfodbs.kantiana.ru/ImtRDB/. It is accompanied by the software calling all types of interspersed repeats with different level of degeneracy in circular DNA. This database and software can become a very useful tool in various areas of mitochondrial and chloroplast DNA research.http://link.springer.com/article/10.1186/s12864-019-5536-1mtDNAImperfect repeatsDatabaseSelection on dinucleotides |
| spellingShingle | Viktor N. Shamanskiy Valeria N. Timonina Konstantin Yu. Popadin Konstantin V. Gunbin ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation BMC Genomics mtDNA Imperfect repeats Database Selection on dinucleotides |
| title | ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation |
| title_full | ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation |
| title_fullStr | ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation |
| title_full_unstemmed | ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation |
| title_short | ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation |
| title_sort | imtrdb a database and software for mitochondrial imperfect interspersed repeats annotation |
| topic | mtDNA Imperfect repeats Database Selection on dinucleotides |
| url | http://link.springer.com/article/10.1186/s12864-019-5536-1 |
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