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GMOD / jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser
https://jbrowse.org/jb2
Apache License 2.0
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Display LTRs of RT-LTR elements, TIRs in Class II elements, and other Transposable element structural features generated by EDTA package #3080

Open amvarani opened 2 years ago

amvarani commented 2 years ago

It would be a nice feature to draw the structural features of transposable elements such as TIRs (Terminal invertead repeats), LTRs (Long Terminal Repeats), and TE related genes (polyproteins) in jBrowser2 Actually, the only tool capable of that is the AnnotationSketch from GenomeTools package (LTR digest), see below an example:

image

Considering that the most reliable annotation tool for Transposable elements, the EDTA (https://github.com/oushujun/EDTA) package is capable to generate a gff3 file containing all the necessary information (below an example), it will be just a matter to parse this gff3 and genetare all TE related features in jBrowser

chr1 EDTA target_site_duplication 2255613 2255617 . + . ID=lTSD_727;Parent=repeat_region_727;Name=TE_00000964;Classification=LTR/Gypsy/Tekay-like;Sequence_ontology=SO:0000434;ltr_identity=0.9608;Method=structural;motif=TGCA;tsd=AGTAA chr1 EDTA long_terminal_repeat 2255618 2256075 . + . ID=lLTR_727;Parent=repeat_region_727;Name=TE_00000964;Classification=LTR/Gypsy/Tekay-like;Sequence_ontology=SO:0000286;ltr_identity=0.9608;Method=structural;motif=TGCA;tsd=AGTAA chr1 EDTA Gypsy_LTR_retrotransposon 2255618 2262037 . + . ID=LTRRT_727;Parent=repeat_region_727;Name=TE_00000964;Classification=LTR/Gypsy/Tekay-like;Sequence_ontology=SO:0002265;ltr_identity=0.9608;Method=structural;motif=TGCA;tsd=A GTAA chr1 EDTA long_terminal_repeat 2261580 2262037 . + . ID=rLTR_727;Parent=repeat_region_727;Name=TE_00000964;Classification=LTR/Gypsy/Tekay-like;Sequence_ontology=SO:0000286;ltr_identity=0.9608;Method=structural;motif=TGCA;tsd=AGTAA chr1 EDTA target_site_duplication 2262038 2262042 . + . ID=rTSD_727;Parent=repeat_region_727;Name=TE_00000964;Classification=LTR/Gypsy/Tekay-like;Sequence_ontology=SO:0000434;ltr_identity=0.9608;Method=structural;motif=TGCA;tsd=AGTAA

This can be possible ?

Best regards

cmdcolin commented 2 years ago

thanks for opening this issue. I had another user ask about this awhile ago but I think we don't have great support for this just yet. we may want to make a specialized glyph for TEs!

amvarani commented 2 years ago

Hi! Thanks for your answer, That will be fantastic Really looking forward to it !

amvarani commented 1 year ago

Hi @cmdcolin Any news regarding that feature? This will help a lot for understanding (visualizing) genes captured by LARDs and Helitrons elements

Best wishes

cmdcolin commented 1 year ago

@amvarani thanks for the reminder :) no updates yet but it is really good to know there is continued interest