Is there a way to find out if a SNP is located in an miRNA coding region?
For example, if I have a list of SNPs, is it possible to find out how many of my SNPs are located in an miRNA coding region using rsID or genomic coordinates as input?
One of the following may work,
http://www.ensembl.org/Homo_sapiens/Tools/VEP
http://snp-nexus.org/guide.html
Hi Veera
If you have a list of SNPs coming from a NGS experiment and processed by a software like snpEff, you should have the genomic coordinates of this SNP and also the gene where it is located. You should check if you have some miRNAs in this gene list and then go to miRbase to see if the SNPs are in the mature sequence. I do not know any tool that does this directly.
Best. Paco
Hi again
There is an old paper where they do something similar finding SNPs at the mIRNA and targets
http://www.pnas.org/content/104/9/3300.full
I'd use the genomic coordinates to search EnsEMBL or miRBase. If it's a lot of SNPs, EnsEMBL has a handy Perl API so you could automate the searches.
I suggest to use Bedtools in this case. Just use intersect to count the overlapping SNPs with miRNA co-ordinates
One of the following may work,
http://www.ensembl.org/Homo_sapiens/Tools/VEP
http://snp-nexus.org/guide.html
There is a good paper from 2012 which might help you here
http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0030737&representation=PDF
You can use the Galaxy. follow these step:
1-Obtain your SNPs coordinate (try dbSNP batch query to do this). The SNP coordinate is zero-based.
2-Download miRNAs coordinate from miRBase. You need to extract the miRNAs mature (miRs) coordinate
.3-upload your files on the Galaxy server. You need to specify your file type. The file type must be interval(A tabular file with columns as chr, start, end, annotation).
4- Try the tool "intersect two intervals" from the Galaxy tools.
Enjoy It.
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biomolecules
- Nucleic Acids
- RNA
- Small RNA
- microRNA