search

zhangrengang / TEsorter

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes
https://doi.org/10.1093/hr/uhac017
GNU General Public License v3.0
85 stars 19 forks source link

Header of the .cls.tsv file #4

Closed oushujun closed 4 years ago

oushujun commented 4 years ago

In the *.cls.tsv file, the header is listed in the following format. However, in the place of "Order", the true classification should be in the "Subclass" level. For the order level, it probably should be "Transposable elements", "telomere", "knobs", "tandem repeats", and something like that.

Class 1 TE: retrotransposons --- subclass: LTR, LINE, SINE, ... Class 2 TE: DNA transposons --- subclass: TIR, Helitron, ...

TE Order Superfamily Clade Complete Strand Domains

Chr10_11341966_11353509#DNA/DTC TIR EnSpm_CACTA unknown unknown + TPase|EnSpm_CACTA Chr10_1407216_1416994#DNA/DTC TIR EnSpm_CACTA unknown unknown - TPase|EnSpm_CACTA Chr10_15280546_15283837#DNA/DTM LTR Copia Ivana no + GAG|Ivana PROT|Ivana Chr10_15702600_15707627#DNA/DTM TIR MuDR_Mutator unknown unknown - TPase|MuDR_Mutator Chr10_18286631_18291104#DNA/DTA LTR Copia Ale no + PROT|Ale Chr10_19224444_19228830#DNA/DTM TIR MuDR_Mutator unknown unknown + TPase|MuDR_Mutator Chr11_23324292_23325763#DNA/DTH mixture mixture unknown unknown ? RH|Ale TPase|hAT Chr11_23650026_23652156#DNA/DTM LTR Gypsy Tekay no + RT|Tekay Chr11_24975696_24980697#DNA/DTM TIR MuDR_Mutator unknown unknown + TPase|MuDR_Mutator Chr2_19381852_19383154#DNA/DTC Helitron unknown unknown unknown + HEL2|Helitron Chr2_21518422_21522564#DNA/DTM LTR Gypsy Reina no + GAG|Reina PROT|Reina

Best, Shujun

zhangrengang commented 4 years ago

@oushujun, based on the classification system by Wicker et al., 2007, these are in the Order level, including LTR, LINE, TIR, Helitron, etc. REXdb also followed these system in Class (Class_I and Class_II) and Sub_class (Subclass_1 and Subclass_2 in Class_II) levels. Despite this system is argued, it is still reasonable.

oushujun commented 4 years ago

Ahh, I was confused and thought the hierarchy was order > class > family. But actually is class > order > family. In this sense, order ~ subclass > superfamily. The original classification is correct.