Why no SINEs, LINEs, LTR and DNA elements were found by Repeatmasker

Question

[qwzhang0601]

Dear all:

I ran RepeatMasker on the mouse genome by using the command "RepeatMasker -species rodentia -pa 5 Mouse.fa -dir MouseRepMaskNew". But I found there were only annotation for "Simple repeats" and "Low complexity". Does anybody have any ideas about this? Many thanks. BTW, the version I am using is "RepeatMasker version open-4.0."

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file name: Mouse.fa
sequences: 21 total length: 2725521370 bp (2647521528 bp excl N/X-runs) GC level: 41.67 %

bases masked: 109540088 bp ( 4.02 %)

number_of_elements length_occupied percentage_of_sequence

SINEs: 0 0 bp 0.00 % Alu/B1 0 0 bp 0.00 % B2-B4 0 0 bp 0.00 % IDs 0 0 bp 0.00 % MIRs 0 0 bp 0.00 %

LINEs: 0 0 bp 0.00 % LINE1 0 0 bp 0.00 % LINE2 0 0 bp 0.00 % L3/CR1 0 0 bp 0.00 %

LTR elements: 0 0 bp 0.00 % ERVL 0 0 bp 0.00 % ERVL-MaLRs 0 0 bp 0.00 % ERV_classI 0 0 bp 0.00 % ERV_classII 0 0 bp 0.00 %

DNA elements: 0 0bp 0.00 % hAT-Charlie 0 0 bp 0.00 % TcMar-Tigger 0 0 bp 0.00 %

Unclassified: 0 0 bp 0.00 %

Total interspersed repeats: 0 bp 0.00 %

Small RNA: 0 0 bp 0.00 %

Satellites: 0 0 bp 0.00 %

Simple repeats: 1779136 93034828 bp 3.41 %

Low complexity: 269822 16576752 bp 0.61 %

• most repeats fragmented by insertions or deletions have been counted as one element

The query species was assumed to be rodentia
RepeatMasker Combined Database: Dfam_Consensus-20170127

run with rmblastn version 2.2.27+

Answer 1

[Charles Warden]

Another option could be to start with some FASTA sequences and see if they have any BLAST similarity: I'm not sure how one type of repeat annotation is selected over another, but a lack of BLAST hits could give confidence in the lack of other repeat elements. You could also run RepeatMasker with a custom database.

Either way, there are a couple way to get repeat sequences:

1) Within RepeatMasker, I believe there should be a queryRepeatDatabase.pl script (in a version that I was using, I see it within a "util" subfolder). You can extract sequences for a species of interest this way.

2) RepBase has some repeat FASTA files, in .ref files separated by species (registration required, but free for non-profits): https://www.girinst.org/downloads/

There are some descriptions of the RepBase repeat families here: https://www.girinst.org/repbase/update/

Otherwise, maybe there really aren't those types of repeats in your sequence?