Hello,
I extracted the DNA of my each 13 inbred mice of C57Bl/6J strain, before and after the behavior experiment, 26 samples in total. During shipping the mice I have lost their ID given before the experiment.
By looking at the specific loci of their DNA samples, I want to find out the ID of my mice. So, which method would be most suitable for matching the two unknown DNA sequences? ( except the whole genome sequencing)
My problem is that all the mice are inbred of C57Bl/6J and are very closely related genetically, so it is very hard for looking SNPs either.
Would really appreciate your suggestions!
str typing like in forensics (but i don't know if there is a database that you could use for help) or sequence mtDNA if the mice are not of the same female.
Hi Abdylla,
There is a recent method for matching the two unknown DNA sequences.It's called Phylogeny Reconstruction which is a fundamental task in computational biology and basic step to estimate pairwise evolutionary distances between protein or nucleic-acid sequences, , there is a detailed protocol in
Article The number of k-mer matches between two DNA sequences as a f...
What do you mean by "having" the DNA of your mice?
DNA won't change (at least not in a non-epigenomical way) before and after your behavioral experiment. So, if you already have sequenced your samples for a single locus all you have to do is to join them using any phylogenetic tree approach. I. e. you can make a tree using the MEGA software.
https://www.megasoftware.net/mega1_manual/Phylogeny.html
Sequences that come from the same sample will be joined in terminal branches.
If you have not sequenced your DNA. I. e. you have done only the extraction of it. Will you sequence it? Or what kind of analysis do you plan to do with your DNA samples? Sequencing of a single gene will most likely give you enough data to look for its pair in your "after experiment" database (but read the last paragraph). And, if you plan to do any next generation sequencing protocol (i.e. RAD-seq) this will absolutely give you enough power; due to the high amount of markers, to identify the pair of each of your DNA samples.
Please note, however, that if you only sequence one locus, it might be possible that two or more of your samples share a single haplotype. This is highly dependent on the genetic diversity of your population of origin, as well as the levels of polymorphism of the locus you are working with (i.e a non coding vs a coding region). In this case, those sequences won't give you the information to distinguish between those samples. In that case you might try using RFLPs to distinguish between those samples using a restriction enzyme and a simple gel electrophoresis (this will be the cheapest option) or maybe genotype your samples using a more polymorphic marker. I. e. a couple of microsatellite loci.
Luis Rodrigo Arce-Valdés, the problem is that all the 13 mice are inbred of C57Bl/6J strain and very close genetically. currently i have their extracted DNA for further analysis. I wanted to look at their SNPs differences on the SNPs dense region "loci" of DNA, but I could not find any literature mentioning about SNPs dense region of C57Bl/6J strain either.
Maybe you know the highest SNPs dense region of C57Bl/6J ? or what method will be most suitable method for me, regarding the price as well?
Thansks for cooperation!
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