lecture_notes:05-27-2015
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lecture_notes:05-27-2015 [2015/05/28 12:23] emfeal |
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| ==== Repeat Annotation ==== | ==== Repeat Annotation ==== | ||
| * Different types of repeats can be studied along with their levels of activity (evolutionary analyses) | * Different types of repeats can be studied along with their levels of activity (evolutionary analyses) | ||
| - | === Types of Repeats === | + | === Types of Repeats === |
| * low-complexity sequence: microsatellites, homopolymers, etc. | * low-complexity sequence: microsatellites, homopolymers, etc. | ||
| - | == Transposable Elements == | + | == Transposable Elements == |
| * class 1: retrotransposon; "copy & paste"; LTR, LINES, SINES | * class 1: retrotransposon; "copy & paste"; LTR, LINES, SINES | ||
| * class 2: DNA transposons; "cut & paste"; subclass 1 and subclass 2 | * class 2: DNA transposons; "cut & paste"; subclass 1 and subclass 2 | ||
| - | === Repeat Content === | + | === Repeat Content === |
| * Does not necessarily correlate with genome size | * Does not necessarily correlate with genome size | ||
| * some correlation within the same group | * some correlation within the same group | ||
| - | === Tools === | + | === Tools === |
| * Homology: RepeatMasker | * Homology: RepeatMasker | ||
| * denovo: RepeatModeler, WindowMasker, RepeatScout, Piler | * denovo: RepeatModeler, WindowMasker, RepeatScout, Piler | ||
lecture_notes/05-27-2015.txt ยท Last modified: 2015/05/28 12:48 by emfeal
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