How to extract hypervariable region of mitochondrial dna from its fasta file?
Recently I've done some analysis on mitochondrial DNA and now I want to run the same analysis on only hypervariable regions of mitochondrial DNA to see whether the changes that I have observed are linked to only hypervariable regions or not. To do that, I'll need to make new fasta files from the mitochondrial DNA entries that I have and I want to know how to extract those. Any leads will be appreciated.
• 1,628 views
•
link
written
by
iamakhilverma •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
whole genome seq for Gazelle - assemble mitochondria
written by m90 •
-
Depth of Coverage in Mitochondrial Genome with Samtools
written by Lida •
-
Extracting region from alternate genome
written by Ana •
-
HISAT2: Required GTF file of LENTINULA EDODES
written by 26amanthk67 •
-
How to integrate the transcriptomics data with kinetic metabolic models?
written by iamakhilverma •
-
Introduction to Structural Bioinformatics
written by iamakhilverma •
-
Where can I find the HVR coordinates of mitochondrial DNA on the human genome?
written by Glen •
-
Control Region Annotation
written by Schmendrick •
-
Remove potential paralogs from BLAST output
written by mforthman •
-
fasta filtering & sorting for SAGE [String-overlap Assembly of GEnomes]
written by adhb •
There are several hypervariable regions in mtDNA, I know about at least two of them.
There is a kit to extract them
https://norgenbiotek.com/sites/default/files/resources/Mitochondrial-DNA-Hypervariable-Region-I-and%20II-Insert-PI52800-1.pdf
See this article, it may help you.
mtDNA Variation and Analysis Using MITOMAP and MITOMASTER
Marie T. Lott, Jeremy N. Leipzig, Olga Derbeneva, H. Michael Xie et al.
https://www.researchgate.net/publication/259891715_mtDNA_Variation_and_Analysis_Using_Mitomap_and_Mitomaster/link/59dce5750f7e9b2120321a9e/download
Also see the post below, and you may try to determine it by yourself.
A: Heteroplasmy detection program