hi everyone I'm dealing with some sequenced genome , my purpose is to design a pipeline to annotate a large numbers of sequence variants throughout the sequenced genomes, for now i'm working on SNP ,a lot of tools and scripts exists to annotate the exonic snps (annovar,dbNSFP,Polyphen,Sift..) ,so my work with this kind SNP is done .
Since these regions (exonic) only account for little fraction of the human genome ,it may be interesting to shift the research efforts on the the intronic snp , snp on splice site ,snp on transcription factor , an idea is to see if a nucleotide is conserved throughout the evolution (alignment between different species) , if it's highly conserved , we could say it's an important allele an its alteration may be affecting the regulation of some gene .
if someone has something to propose for the in silico study of non exonic snp (intronic ,utr 3 , utr 5 , intergenic) ,please share your ideas .
2 answers
Annovar does not only work on exons. It will also perform region-based annotation and consider the types of thing you mention (transcription factor binding sites, conserved regions etc).
http://www.openbioinformatics.org/annovar/annovar_region.html
You should look at the responses to this question on investigating the functional consequence of SNPs. I'd pretty much give you the same answer I gave then. It is not in your list above, but synonymous SNPs are also interesting - see the responses to a question on this topic as it may be good for you to consider as well.
Intronic SNPs will have an effect on gene expression, especially those that map to intron 1, and on splicing. In some rare cases, the intronic SNP will map to another gene contained within that intron. Some of these are microRNAs, like miR-33A.
Intergenic SNPs need to be thought of as affecting enhancer activity. There are loads of databases on this. Basically, you'd like to see if the SNP maps to known enhancers or regions of differential (i.e, tissue specific) histone or DNA methylation sites.
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