Yes, you can find single nucleotide polymorphisms in many species at a time, it will represent at least 1 difference after 1.1 million bases in DNA molecule. These may located differently in different species. Detecting Single Nucleotide Polymorphisms (SNPs) between genomes is becoming a routine task with Next Generation Sequencing. Generally, SNP detection methods use a reference genome. As nonmodel organisms are increasingly investigated, the need for reference-free methods has been amplified. Most of the existing reference-free methods have

fundamental limitations: they can only call SNPs between exactly two datasets, and/or they require a prohibitive amount of computational resources. The method we propose, DISCOSNP, detects both heterozygous and homozygous isolated SNPs from any number of read datasets, without a reference genome, and with very low memory and time footprints (billions of reads can be analyzed with a standard desktop computer). To facilitate downstream genotyping analyses, DISCOSNP ranks

predictions and outputs quality and coverage per allele. Compared to finding isolated SNPs using a state-of-the-art assembly and mapping approach, DISCOSNP requires significantly less computational resources, shows similar precision/recall values,

and highly ranked predictions are less likely to be false positives. Experimental these are predicted in arthropod species (the tick Ixodes ricinus) on which de novo sequencing was performed. Among the predicted SNPs tested, 96% were successfully genotyped and truly exhibited polymorphism.

Dear Ravi,

Many thanks for your very accurate and useful reply. I will take into account to use DISCOSNP for my purposes. The NGS field of science is a new area of knowledge for me, but your suggestion is really useful to me. It will help me to clearly plan the analysis of my current "early-stage" project on comparative genomics!

Thanks again.

Cheers!

Paolo

Hi Stew,

Thank you really much for your reply! It is helpful, of course! I'm planning a research proposal about comparative genomics, in order to contrast genomes in fish species that evolved different life history traits. Since I'm a beginner in genomics, I thought to ask about feasibility of my proposal. I'm glad to know that my idea may be executable.

Thank you, again!!

Paolo 

Dear Paolo,

I'm also interested in this question you asked 4 years ago. Have you got your answer or solution yet?

By the way, i'm also working in Roscoff doing my phD study. Seems we've met before and had a nice talk together. I wonder if we can have a talk again. Let me know if it's possible. Looking forward to your answer.

Ruibo