Ltr insertion time about ltr_retriever HOT 26 CLOSED

Hi @U201412486,

Please see the information above. If you can find divergence or identity in the gff3 file, then you can calculate the insertion time by hand or excel with T = K/2µ, K is the divergence of the LTR = 1 - identity.

Best,
Shujun

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Hi,
I have the LTR gff3 file.
How should I do If I just want to use LTR_retriever to compute the insertion time of the LTR ?
Thanks,
sun,

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@oushujun Thank you for your answer.
I need to caculate sequence identity between the 5' and 3' direct repeats of an LTR candidate firstly.I do not know how to extract 5' and 3' direct repeats sequnce of an LTR.Can you give me advice?
many thanks,
sun

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The LTR_retriever/bin/call_seq_by_list.pl can be used to extract sequences accroding to the coordinate.So how can I get the coordinate of the 5' and 3' direct repeats of an LTR? The thing is that I do not know how to idenified the coordinates of the 5' and 3' direct repeats of an LTR.

Best,
sun

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Thank you so much.
Can you tell me the process of extracting the 5' and 3' direct repeats of an LTR such as any script ?

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Dear Dr. Ou Shu Jun,
Can I use the unit of "Insertion_Time" as Milion Years Ago (MYA) by dividing the result by 10,00,000?
Fo eg., 595557 as 0.595 MYA ?

Thanking you!
Regards,
Prabhu, S

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@Prabhu89-code Yes you can. You can even reestimte the time with the mutation rate of your species (µ, per bp per year) using the identity with T = (1 - identity%) / 2µ.

Best,
Shujun

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Thank you for your reply Dr. Shu Jun.
I have never done mutation rate and insertion time calculation. I am working in Peach. I will try to collect information from literatures and reestimate with the formula you mentioned.

Thanking you!

Regards,
Prabhu, S

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Dear Dr. Shu Jun,
What about the identity percentage of 1. How do we estimate those LTR's insertion time.

Thanking you !

Regards,
Prabhu, S

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So, the age of '0' is correct ? What it means in terms of insertion time.

-Prabhu

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Dear Dr. Shu Jun,
Thank you very much for your clarification. Now I understood it completely. Your answers are so helpful in understanding about LTR.

Thanking you!

Regards,
Prabhu, S

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Hello shujun, @oushujun

I noticed that some identities in the LTR_Retriever result file are less than 0.01, and then the insertion_time column shows up as "NA". How do you explain this?

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Hello @wensulin93,

Do you see all of them or just a portion of them showing the identity less than 0.01? Has this file been modified after LTR_retriever generated it? Thank you.

Best,
Shujun

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hello， @oushujun

Only part of it. There are dozens of them out of thousands, as shown in the picture. And only below 0.01 (jump directly from 0.9 to 0.01). The LTR_Retriever version I'm using is 2.9.0. Because I'm involved in calculating the insertion time, but if you start with identity value < 0.01 for insertion time would show significant outliers over billions of years (second picture), which is clearly not possible. Then I noticed that in gCA_019656295.1_rRI_R1.1_genom.fna.mod.pass, the default insertion time value (Identity < 0.01) is NA, so I excluded these identity <0.01 in my subsequent continuation. Then the distribution of insertion time seemed normal. It also seems that TEsorter can rule out these outliers.

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Hi,

Can you send me the .defalse file to further check on these candidates? Thank you.

Shujun
[email protected]

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Hi,

Can you send me the .defalse file to further check on these candidates? Thank you.

Shujun [email protected]

Has been sent.

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Hi,

Can you send me the .defalse file to further check on these candidates? Thank you.

Shujun [email protected]

Hello, @oushujun

Upon inspection, it looks like that the reason is LTR_Retriever running on the PC（Core i5-9400F，6 CORES, 16GB RAM）. Initially I was running on a PC and got a lot of "<0.01 identity", as shown below.

But once I ran it on the server (120G RAM, 40 CORES), there were almost no items less than 0.01 identity, as shown below。

Is LTR_Retriever automatically skipping hard-to-handle projects due to computer capabilities? Please refer to and add appropriate instructions in the main page. Due to network reasons and time constraints, LTR_Retriever cannot be run for PC for further testing. I will further test in my spare time and inform you of the results!

By the way, the BLASTN version on the server is 2.5.0+; On the PC, it's 2.12.0+.

Thank you very much!

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Hi,
Can you send me the .defalse file to further check on these candidates? Thank you.
Shujun [email protected]

Hello, @oushujun

Upon inspection, it looks like that the reason is LTR_Retriever running on the PC（Core i5-9400F，6 CORES, 16GB RAM）. Initially I was running on a PC and got a lot of "<0.01 identity", as shown below.

But once I ran it on the server (120G RAM, 40 CORES), there were almost no items less than 0.01 identity, as shown below。

Is LTR_Retriever automatically skipping hard-to-handle projects due to computer capabilities? Please refer to and add appropriate instructions in the main page. Due to network reasons and time constraints, LTR_Retriever cannot be run for PC for further testing. I will further test in my spare time and inform you of the results!

By the way, the BLASTN version on the server is 2.5.0+; On the PC, it's 2.12.0+.

Thank you very much!

Hi,
Can you send me the .defalse file to further check on these candidates? Thank you.
Shujun [email protected]

Hello, @oushujun

Upon inspection, it looks like that the reason is LTR_Retriever running on the PC（Core i5-9400F，6 CORES, 16GB RAM）. Initially I was running on a PC and got a lot of "<0.01 identity", as shown below.

But once I ran it on the server (120G RAM, 40 CORES), there were almost no items less than 0.01 identity, as shown below。

Is LTR_Retriever automatically skipping hard-to-handle projects due to computer capabilities? Please refer to and add appropriate instructions in the main page. Due to network reasons and time constraints, LTR_Retriever cannot be run for PC for further testing. I will further test in my spare time and inform you of the results!

By the way, the BLASTN version on the server is 2.5.0+; On the PC, it's 2.12.0+.

Thank you very much!

This was a previous question, but I recently tried running LTR-Retriever in my PC. I use a virtual machine, linux system, ubuntu. Results showed no abnormalities. different from the previous ones. I deliberately put the files required for running on the hard disk in the virtual machine to run (it was run on a shared hard disk before.). The results show that there are only a few LTRs (3) with Identity<0.01, indicating that the software runs without problems. Maybe it was because the running file was placed in the shared folder before? In short, the LTR_Retriever running on the PC is displayed normally. Although some of the analysis I usually do in the biographies is mainly done on the server.

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Hello, @oushujun
If the -u parameter is not added, is the default evolutionary rate calculated for rice 1.3e-8?

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