Detecting NUMTS (nuclear mitochondrial sequences) in the whole genome sequenced data
Entering edit mode
10 months ago
jigarnt ▴ 30

Hi All,

I want to detect NUMTS (nuclear mitochondrial sequences) that have migrated from the mitochondrial to the nuclear genome using the whole genome sequence data. What could be the best Bioinformatic approach ?? Their presence, extent and frequency of migration of mitoDNA into nuclear DNA is unknown.

Currently, I am trying to align the raw sequenced data with the nuclear reference genome followed by the command line BLAST where I use the mitochondrial genome as Query against the database of nuclear reference genome of the same species. Is that the correct approach ?

For context, about 90% of the mitochondrial genome is susceptible to insertion into the nuclear genome. These insertion events occur throughout an individual's lifespan with regular frequency (usually in DSB repair), and have been occurring for basically the entirety of organism evolution.

Thank you in advance for all your helpful suggestions and comments.

NuMTs genomemining pseudogenes mitochondrialgenome Bioinformatics • 336 views
Entering edit mode
10 months ago
d-cameron ★ 2.6k

Have your considered svaNUMT?


Login before adding your answer.

Traffic: 1685 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6