Inquiry Regarding REXdb 4.0 Implementation in TEsorter

[amvarani]

Hi there,
I am writing to inquire whether there is any estimated timeline for the implementation of REXdb 4.0 in TEsorter.

Thank you for your time developing this excellent and very useful software!

[zhangrengang]

Great! I will update the REXdb 4.0 before the next month.

[zhangrengang]

I have updated the REXdb v4, which is the default option since TEsorter v1.5.0.
Some new clades/domains are added by REXdb v4:

$ diff new-rexdb old_rexdb
31,35d30
< NAME  Class_I/LTR/Ty1_copia/Alexandra:Ty1-GAG
< NAME  Class_I/LTR/Ty1_copia/Alexandra:Ty1-INT
< NAME  Class_I/LTR/Ty1_copia/Alexandra:Ty1-PROT
< NAME  Class_I/LTR/Ty1_copia/Alexandra:Ty1-RH
< NAME  Class_I/LTR/Ty1_copia/Alexandra:Ty1-RT
46,50d40
< NAME  Class_I/LTR/Ty1_copia/Bryana:Ty1-GAG
< NAME  Class_I/LTR/Ty1_copia/Bryana:Ty1-INT
< NAME  Class_I/LTR/Ty1_copia/Bryana:Ty1-PROT
< NAME  Class_I/LTR/Ty1_copia/Bryana:Ty1-RH
< NAME  Class_I/LTR/Ty1_copia/Bryana:Ty1-RT
56,60d45
< NAME  Class_I/LTR/Ty1_copia/Ferco:Ty1-GAG
< NAME  Class_I/LTR/Ty1_copia/Ferco:Ty1-INT
< NAME  Class_I/LTR/Ty1_copia/Ferco:Ty1-PROT
< NAME  Class_I/LTR/Ty1_copia/Ferco:Ty1-RH
< NAME  Class_I/LTR/Ty1_copia/Ferco:Ty1-RT
146,151d130
< NAME  Class_I/LTR/Ty3_gypsy/chromovirus/Ferney:Ty3-CHD
< NAME  Class_I/LTR/Ty3_gypsy/chromovirus/Ferney:Ty3-GAG
< NAME  Class_I/LTR/Ty3_gypsy/chromovirus/Ferney:Ty3-INT
< NAME  Class_I/LTR/Ty3_gypsy/chromovirus/Ferney:Ty3-PROT
< NAME  Class_I/LTR/Ty3_gypsy/chromovirus/Ferney:Ty3-RH
< NAME  Class_I/LTR/Ty3_gypsy/chromovirus/Ferney:Ty3-RT
186,191d164
< NAME  Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tatius:Ty3-aRH
< NAME  Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tatius:Ty3-GAG
< NAME  Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tatius:Ty3-INT
< NAME  Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tatius:Ty3-PROT
< NAME  Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tatius:Ty3-RH
< NAME  Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tatius:Ty3-RT


$ diff new-rexdb-plant old-rexdb-plant
31,35d30
< NAME  Class_I/LTR/Ty1_copia/Alexandra:Ty1-GAG
< NAME  Class_I/LTR/Ty1_copia/Alexandra:Ty1-INT
< NAME  Class_I/LTR/Ty1_copia/Alexandra:Ty1-PROT
< NAME  Class_I/LTR/Ty1_copia/Alexandra:Ty1-RH
< NAME  Class_I/LTR/Ty1_copia/Alexandra:Ty1-RT
46,50d40
< NAME  Class_I/LTR/Ty1_copia/Bryana:Ty1-GAG
< NAME  Class_I/LTR/Ty1_copia/Bryana:Ty1-INT
< NAME  Class_I/LTR/Ty1_copia/Bryana:Ty1-PROT
< NAME  Class_I/LTR/Ty1_copia/Bryana:Ty1-RH
< NAME  Class_I/LTR/Ty1_copia/Bryana:Ty1-RT
56,60d45
< NAME  Class_I/LTR/Ty1_copia/Ferco:Ty1-GAG
< NAME  Class_I/LTR/Ty1_copia/Ferco:Ty1-INT
< NAME  Class_I/LTR/Ty1_copia/Ferco:Ty1-PROT
< NAME  Class_I/LTR/Ty1_copia/Ferco:Ty1-RH
< NAME  Class_I/LTR/Ty1_copia/Ferco:Ty1-RT
146,151d130
< NAME  Class_I/LTR/Ty3_gypsy/chromovirus/Ferney:Ty3-CHD
< NAME  Class_I/LTR/Ty3_gypsy/chromovirus/Ferney:Ty3-GAG
< NAME  Class_I/LTR/Ty3_gypsy/chromovirus/Ferney:Ty3-INT
< NAME  Class_I/LTR/Ty3_gypsy/chromovirus/Ferney:Ty3-PROT
< NAME  Class_I/LTR/Ty3_gypsy/chromovirus/Ferney:Ty3-RH
< NAME  Class_I/LTR/Ty3_gypsy/chromovirus/Ferney:Ty3-RT
186,191d164
< NAME  Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tatius:Ty3-aRH
< NAME  Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tatius:Ty3-GAG
< NAME  Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tatius:Ty3-INT
< NAME  Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tatius:Ty3-PROT
< NAME  Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tatius:Ty3-RH
< NAME  Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tatius:Ty3-RT


$ diff new-rexdb-metazoa old-rexdb-metazoa
4,15d3
< NAME  Class_II/Subclass_1/TIR/Academ:Academ-TPase
< NAME  Class_II/Subclass_1/TIR/EnSpm_CACTA:Cacta-TPase
< NAME  Class_II/Subclass_1/TIR/Ginger:Ginger-TPase
< NAME  Class_II/Subclass_1/TIR/Merlin:Merlin-TPase
< NAME  Class_II/Subclass_1/TIR/PIF_Harbinger:PIF/Harbinger-TPase
< NAME  Class_II/Subclass_1/TIR/PiggyBac:PiggyBac-TPase
< NAME  Class_II/Subclass_1/TIR/P:P-TPase
< NAME  Class_II/Subclass_1/TIR/Sola1:Sola1-TPase
< NAME  Class_II/Subclass_1/TIR/Sola2:Sola2-TPase
< NAME  Class_II/Subclass_1/TIR/Sola3:Sola3-TPase
< NAME  Class_II/Subclass_1/TIR/Transib:Transib-TPase
< NAME  Class_II/Subclass_1/TIR/Zator:Zator-TPase
45a34
> NAME  NA:Retrovirus-RH

However, only slight differences are seen for the rice TE library:

$ diff rice6.9.5.liban.rexdb-v4.cls.tsv rice6.9.5.liban.rexdb-v3.cls.tsv
51c51
< Os0162_INT#LTR/Gypsy  LTR     Gypsy   Athila  no      +       GAG|Athila RT|Athila RH|Athila INT|Athila
---
> Os0162_INT#LTR/Gypsy  LTR     Gypsy   Athila  yes     +       GAG|Athila PROT|Athila RT|Athila RH|Athila INT|Athila
177d176
< Os0883_INT#LTR/Gypsy  TIR     Ginger  unknown unknown +       TPase|Ginger

[amvarani]

That is great! thank you !