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HajkD / LTRpred

De novo annotation of young retrotransposons
https://hajkd.github.io/LTRpred/
GNU General Public License v2.0
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could LTRpred detect DIRS/DIRS in genome contigs? #9

Closed wangj2009 closed 4 years ago

wangj2009 commented 4 years ago

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  1. Could LTRpred detect DIRS/DIRS?
  2. Does LTRpred care about the LTR direction?
  3. Does LTRpred care about the length of TSD? Could I set the parameter as mindistltr = 1000?
  4. LTRpred use the default parameter overlaps = "all", but could I set the parameter as overlaps = "best"?
  5. Are there any other parameters need to be set?
  6. Are there some softwares to annotate DIRS/DIRS except LTRpred? Thanks,
HajkD commented 4 years ago

Could LTRpred detect DIRS/DIRS?

It won't detect inverted LTRs, but for same directional LTRs you could specify the correct protein domains that characterize for DIRS and screen for them with LTRpred

Does LTRpred care about the LTR direction?

yes

Does LTRpred care about the length of TSD? Could I set the parameter as mindistltr = 1000?

yes, see parameters min_tsd, max_tsd

LTRpred use the default parameter overlaps = "all", but could I set the parameter as overlaps = "best"?

yes, see the documentation in R ?LTRpred::LTRpred

Are there any other parameters need to be set?

https://hajkd.github.io/LTRpred/articles/Introduction.html

Are there some softwares to annotate DIRS/DIRS except LTRpred?

I am sure there are.

wangj2009 commented 4 years ago

Could you suggest some other software to annotate the structure of DIRS/DIRS? Thanks,

HajkD commented 4 years ago

Unfortunately not. I never worked with DIRS. Hope this helps.