search

oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
177 stars 40 forks source link

LTR age using local TE library seq #64

Closed bioteksampath closed 4 years ago

bioteksampath commented 4 years ago

Hi oushujun,

wondering if you give suggestions on how to calculate age of LTRs from previously published genomes (wheat).

I have the TE gff (with complete and fragment information) but I don't have 3' or 5' LTR position information. I like to calculate the age of each LTR, so wondering how can I use the local TE library in LTR retriever to get an age for each element?

Any suggestions would be helpful.

Thanks sam

oushujun commented 4 years ago

Hi Sam,

You can extract the intact LTR sequence from the gff, do a self blast for each sequence, within each blast result, you may find the pairing of the 5' and 3' LTR and the identity between them, then use this equation to calculate the age: T = (1- iden%) / 2µ with µ being the mutation rate you prefer.

Hope this helps!

Best, Shujun

oushujun commented 4 years ago

Close for now due to inactive. Please reopen if you have more questions.