Where can I find a fasta for mitochondrial genes?

Question

[blur]

Hi,

I want to align reads to the mm10 and hg19 mitochondrial genes. Were can I get the fasta file for all these genes as a reference?

I found this: https://www.ncbi.nlm.nih.gov/genome/51?genome_assembly_id=1559677 but I don't think it will give me the genes... Any help would be appreciated

[Jorge Amigo]

Note that hg19 mtDNA is not the rCRS. This one was already present in GRCh37, which is one of the differences between hg19 and GRCh37, and is now in hg38.

Answer 1

[GenoMax]

Method 1:

1. Download relevant annotation files from GENCODE. Human hg19 and Mouse mm10
2. Fish out Ensembl ID's of the genes from each file awk -F "\"" '$1 ~ /chrM/ && $3 ~ /gene/ {print $2}' gencode.v37lift37.annotation.gtf (this is hg19 example)
3. Use BioMart to retrieve sequence

Method 2:

1. Download annotation file from NCBI. Human hg19 or Mouse mm10

2. Get the sequence using EntrezDirect
   awk -F "\t" '$1 ~ /NC_012920/ && $3 ~ /gene/ {print $1,$4,$5}' GRCh37_latest_genomic.gff | xargs -n 3 sh -c 'efetch -db nuccore -id "$0" -seq_start "$1" -seq_stop "$2" -format fasta' (human hg19)

3. For mouse mm10
   awk -F "\t" '$1 ~ /NC_005089/ && $3 ~ /gene/ {print $1,$4,$5}' GCF_000001635.26_GRCm38.p6_genomic.gtf | xargs -n 3 sh -c 'efetch -db nuccore -id "$0" -seq_start "$1" -seq_stop "$2" -format fasta'

[ATpoint]

For Method 1 you could directly download the transcriptome fasta files from Gencode and pull the cDNA/spliced sequences from there (if this is what you want rather than the entire genomic gene sequence incl introns).

Answer 2

[m3hdad]

There are different tools and repositories. GRCh37 (hg19) has been archived on Ensembl.

Here are some tips:

• Make sure you have a good reason why you don't want to align your reads against an updated version.
• Make sure you understand what "fasta" and "gtf/gff" files are.

Some tools you might want to read about are:

• BSgenome
• Biomart

Good luck and I think finding data for mm10 should be straight forward now.