Global Repeat Map (GRM) Application: Finding All DNA Tandem Repeat Units
Abstract
:1. Introduction
2. Materials and Methods
2.1. Algorithm Outline
2.2. Application Usage and Output
3. Results
3.1. Human Chromosome 19
3.2. Comparison of Human, Chimp and Mouse Chromosome 19 GRM Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Loc | Type | Name | RefSeq | INSDC | Size (Mb) | GC% | Protein | rRNA | tRNA | Other RNA | Gene | Pseudogene |
---|---|---|---|---|---|---|---|---|---|---|---|---|
Homo sapiens | Chr | 19 | NC_000019.10 | CM000681.2 | 58.62 | 47.9 | 6944 | - | 6 | 2001 | 2494 | 527 |
Pan troglodytes | Chr | 19 | NC_036898.1 | CM009257.2 | 56.73 | 48.4 | 4949 | - | 7 | 834 | 1997 | 213 |
Mus musculus | Chr | 19 | NC_000085.7 | CM001012.3 | 61.42 | 43.1 | 2718 | - | 9 | 1041 | 1380 | 229 |
TR Unit (bp) | No. Copies | Start (bp) | End (bp) | CG(%) |
---|---|---|---|---|
172 | 163 | 24,203,386 | 24,231,348 | 36.1 |
172 | 30 | 24,237,553 | 24,242,705 | 36.1 |
172 | 66 | 24,252,398 | 24,263,766 | 36.7 |
172 | 23 | 24,273,657 | 24,279,543 | 37.5 |
172 | 197 | 24,286,112 | 24,320,483 | 36.1 |
172 | 362 | 24,329,796 | 24,394,003 | 36.2 |
171 | 32 | 24,400,265 | 24,405,823 | 36.0 |
2896 | 12 | 24,412,442 | 24,447,210 | 38.1 |
171 | 2302 | 24,499,052 | 24,891,328 | 39.3 |
340 | 6721 | 24,905,001 | 27,190,218 | 39.2 |
340 | 41 | 27,241,096 | 27,255,422 | 37.5 |
171 | 132 | 27,258,016 | 27,280,642 | 36.3 |
171 | 163 | 27,286,672 | 27,318,118 | 36.1 |
171 | 19 | 27,321,147 | 27,324,392 | 36.8 |
171 | 383 | 27,330,489 | 27,421,643 | 36.1 |
172 | 187 | 27,428,565 | 27,463,476 | 36.0 |
172 | 80 | 27,469,901 | 27,500,339 | 36.2 |
172 | 57 | 27,505,176 | 27,514,962 | 37.0 |
172 | 335 | 27,520,248 | 27,577,951 | 36.0 |
172 | 80 | 27,583,082 | 27,596,854 | 36.6 |
172 | 174 | 27,603,075 | 27,632,964 | 35.9 |
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Glunčić, M.; Vlahović, I.; Mršić, L.; Paar, V. Global Repeat Map (GRM) Application: Finding All DNA Tandem Repeat Units. Algorithms 2022, 15, 458. https://doi.org/10.3390/a15120458
Glunčić M, Vlahović I, Mršić L, Paar V. Global Repeat Map (GRM) Application: Finding All DNA Tandem Repeat Units. Algorithms. 2022; 15(12):458. https://doi.org/10.3390/a15120458
Chicago/Turabian StyleGlunčić, Matko, Ines Vlahović, Leo Mršić, and Vladimir Paar. 2022. "Global Repeat Map (GRM) Application: Finding All DNA Tandem Repeat Units" Algorithms 15, no. 12: 458. https://doi.org/10.3390/a15120458