Question: Find unique genes in mouse genome with no homology to human genome.
1
gravatar for Ron
3.4 years ago by
Ron910
United States
Ron910 wrote:

Hi all,

I have DNA sequencing data where human tumors have mouse reads as per the experiment protocol(similar to PDX).

I have calculated the read counts of these mouse genes. using HTSEQ-count,after this I want to select only those mouse genes which have no homology to the human genome and only mouse specific.

Is there any tool to do this besides BLAST?Let me know.

Thanks,

Ron

sequence gene • 1.8k views
ADD COMMENTlink modified 3.4 years ago by h.mon24k • written 3.4 years ago by Ron910

How many genes are unique to mouse and not found in humans? I don't imagine that number is high.

I think it would be easier to create a database of mouse-specific genes first and then use that to extract the sequences you're interested in.

ADD REPLYlink written 3.4 years ago by jotan1.2k
5
gravatar for h.mon
3.4 years ago by
h.mon24k
Brazil
h.mon24k wrote:

Find all the orthologous genes between the two species (one database of many here, one how-to here), the mouse genes not present in this list are the genes you want.

ADD COMMENTlink written 3.4 years ago by h.mon24k
1

There's actually an easier way than the BioMart tutorial you give. Instead of finding all the homologues, filter by Othologous Human Genes, Excluded.

ADD REPLYlink written 3.4 years ago by Emily_Ensembl17k
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