How to discover "sequencing gaps" in genome assemblies. about ltr_retriever

[Wenwen012345]

Hello, maybe I thought of a way. You can BLAST the DNA sequence on NCBI. Generally speaking, if these genes really exist, BLAST will have the result of homologous alignment. And if the BLAST results are visualized, there should be a reasonable correspondence, and the "empty part" should be the part where the transposon is inserted.

[oushujun]

Hello,

I am glad LTR_retriever is helping you to find our biologically meaningful markers! Your question is a bit off topic, but I think your proposed ways (PCR, no 'N', BLAST) should work especially with multiple evidence combined.

Best,
Shujun

[Wenwen012345]

Thanks! This guy tried it. The manuscript is somewhat related to graduation, so the guy has carefully considered this issue.