http://rnirmal.com/docs/repclass_theses

2.4.3 Long Terminal Repeats (LTR) ...................................................................... 20 2.4.4 Simple Sequence Repeats (SSR) ................................................................... 21 2.4.5 tRNA Structure .............................................................................................. 21 2.5 Identification of Transposable Elements .............................................................. 22 2.6 Genome Sequence Analysis ................................................................................. 23 2.7 Identification and annotation tools ....................................................................... 24 2.7.1 RECON.......................................................................................................... 24 2.7.2 Piler................................................................................................................ 24 2.7.3 ReAS.............................................................................................................. 25 2.7.4 RepeatScout ................................................................................................... 25 2.7.5 Repeat Masker ............................................................................................... 25 2.8 Cluster and Grid computing ................................................................................. 26 2.9 Clusters and Bioinformatics ................................................................................. 27 3. REPCLASS................................................................................................................. 28 3.1 De novo identification of repeat families ............................................................. 29 3.2 Automated REPCLASS workflow ....................................................................... 30 3.3 Homology based classification............................................................................. 32 3.3.1 Homology Search .......................................................................................... 32 3.4 TSD based classification ...................................................................................... 35 3.4.1 TSD Search .................................................................................................... 35 3.4.2 Helitron Scan ................................................................................................. 37 3.5 Structural properties based classification ............................................................. 39 vi