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oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
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Are "Unknowns" Unknown TEs or generally unknown repeats? #390

Closed isabelladistefano closed 9 months ago

isabelladistefano commented 9 months ago

Dear Shujun,

I am summarising TEs in three species and wonder whethter to include the Unknown results as Unknown TEs or any type of repeat region?

They are SO:0000657 http://sequenceontology.org/browser/current_svn/term/SO:0000657 which say the "children" could be:

nested_repeat (SO:0001649) direct_repeat (SO:0000314) inverted_repeat (SO:0000294) long_terminal_repeat (SO:0000286) non_LTR_retrotransposon_polymeric_tract (SO:0000433) flanking_repeat (SO:0002192) X_element_combinatorial_repeat (SO:0001484) tandem_repeat (SO:0000705) knob (SO:0002257) Y_prime_element (SO:0001485) telomeric_repeat (SO:0001496) centromeric_repeat (SO:0001797) terminal_repeat (SO:0002201) dispersed_repeat (SO:0000658) engineered_foreign_repetitive_element (SO:0000293)

I have read the QandA, but I am wondering if EDTA only picks up certain types of these "children"

Best wishes,

Isabella

oushujun commented 9 months ago

HI Isabella,

It's unknown repeat, which could be TEs or non-TE repeats but EDTA could not find information to further classify them.

Shujun

On Fri, Sep 22, 2023 at 11:11 AM isabelladistefano @.***> wrote:

Dear Shujun,

I am summarising TEs in three species and wonder whethter to include the Unknown results as Unknown TEs or any type of repeat region?

They are SO:0000657 http://sequenceontology.org/browser/current_svn/term/SO:0000657 which say the "children" could be:

nested_repeat (SO:0001649) direct_repeat (SO:0000314) inverted_repeat (SO:0000294) long_terminal_repeat (SO:0000286) non_LTR_retrotransposon_polymeric_tract (SO:0000433) flanking_repeat (SO:0002192) X_element_combinatorial_repeat (SO:0001484) tandem_repeat (SO:0000705) knob (SO:0002257) Y_prime_element (SO:0001485) telomeric_repeat (SO:0001496) centromeric_repeat (SO:0001797) terminal_repeat (SO:0002201) dispersed_repeat (SO:0000658) engineered_foreign_repetitive_element (SO:0000293)

I have read the QandA, but I am wondering if EDTA only picks up certain types of these "children"

Best wishes,

Isabella

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/390, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NAV7VRH5RDFTDX4UETX3WTBLANCNFSM6AAAAAA5DIDOOQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

isabelladistefano commented 9 months ago

Thank you.

As this list from SO only mentions RNA transposons, does this mean that these particular Unknowns are definitely not of a DNA transposon nature?

Best wishes,

Isabella

oushujun commented 9 months ago

No, it can also be DNA transposons but there isn’t any evidence to tell. All TEs can belong under the dispersed repeat child SO.

Thanks, Shujun

On Sat, Sep 23, 2023 at 8:58 AM isabelladistefano @.***> wrote:

Thank you.

As this list from SO only mentions RNA transposons, does this mean that these particular Unknowns are definitely not of a DNA transposon nature?

Best wishes,

Isabella

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/390#issuecomment-1732312985, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NANOMQRTUN7AABRSODX33MG5ANCNFSM6AAAAAA5DIDOOQ . You are receiving this because you commented.Message ID: @.***>