Hello everyone,

I am currently working on identifying Nuclear Mitochondrial DNA segments (NUMTs) in my research. Here is a brief overview of what I have done so far: Steps I Have Completed:

1. Created a BLAST database from the mitochondrial DNA (mtDNA) sequences using the following command:

makeblastdb -dbtype nucl -in mt.fa -out mito blastn -query genome.fa -out Blast.out -db mito -outfmt 6 -evalue 1e-6

Results:

The results from the BLASTn alignment are saved in Blast.out with the following headers:

> Query ID Subject ID Identity Alignment Length Mismatches Gap Opens Query Start Query End Subject Start Subject End E-value Bit Score

query1234 subjectA 84.5 1500 120 30 100 1600 2000 3500 1e-10 1000 query5678 subjectB 88.0 900 85 10 50 950 10000 10900 5e-20 900 query91011 subjectC 87.2 2500 210 40 300 2800 4000 6500 2e-15 1200 query1213 subjectD 90.1 3100 190 50 400 3500 5000 8100 1e-25 1300 query1415 subjectE 82.9 1800 150 20 150 1950 6000 7800 8e-12 950 query1617 subjectF 86.7 700 60 15 200 900 9000 9700 4e-18 850 query1819 subjectG 89.4 210 20 5 100 310 3000 3200 3e-08 300 query2021 subjectH 85.5 2700 250 30 500 3200 8000 10700 1e-22 1250

Next Steps:

I am seeking guidance on the process of identifying NUMTs and creating graphs for analysis. Please provide step-by-step instructions on how to proceed. "Should I filter the results?"

Any guidance or resources you can provide would be greatly appreciated!

Thank you!