Hi friends,
I have got two excelsheets containing the position of synonmous and non-synonmous mutations between human and chimp. And I have found synonmous mutations are less than that of non-synonmous mutations. Now how can I interpret the result from the given output? Please help.
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written
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Haritha •
2 answers
The ratio between these quantities is a proxy for the kind of selection operating on the gene/segment/chromosome. A SNP can result in synonymous, non-synonymous substitution or neither (if outside protein coding sequences). Of course, selection can operate outside exons but the way to measure it is totally different in this case. For the interpretation of synonymouns vs. non-synonymous you should check initially Wikipedia.
Hi!
Haritha could you elaborate your question it is very confusing... you are talking of SNPs and then comparative genomics (b/w human and Chimp)... It will be helpful to formulate an answer for your question if you give us substantial information about the problem.
Anyways, two of the commmonly used computational tool for nsSNP analysis are SIFt and PolyPhen, it is advisable to use both of them as they are complimentary in their approach. while sSNPs can be evaluated using FASTSNP webserver. (This is a very generic anmswer, a precise answer to your question requires more details from your side).
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You can interpret there are more non-synonymous SNPs than synonymous SNPs. You will need to provide more information about the question you want answered before anyone can help you.
You can interpret there are less synonymous SNPs than non-synonymous SNPs. You will need to provide more information about the question you want answered before anyone can help you.
What kind of experiment has this come from?
What results were you expecting?
the data obtained is form comparative analysis of human and chimpanzee's sequences.
So do you want to predict the effect of the changes? What do you want to do with the data set?
Sorry, but these most likely are not SNPs in the sense of the definiton, if they are not the result of a population study, but the comparison of the genome sequences.
There are no SNPs shared between human and chimp. See How To Find Out The Snps Which Are Present In Human And Are Also Present In Other Organisms?
Edited title, question, and tags to reflect that this question is NOT about SNPs but about synonymous vs. non-synonymous mutations between human and chimp.
@Giovanni - your claim that there are no SNPs shared between human and chimp is not strictly true -- there is evidence for trans-specific polymorphism at HLA: http://www.ncbi.nlm.nih.gov/pubmed/2460344
@Casey, I was wondering how much confidence one could have in the findings of this article, as it is from 1988 long before the availability of any full genome sequence. No, criticism, just curiosity.
@Michael - my feeling is that it is probably correct. It's a textbook example of trans-specific polymorphism that has not been overturned in over two decades. But I agree that it is probably worth revisiting this issue and perhaps looking for any other loci that show shared human-chimp alleles in the 1000+ genomes era.