I have got a sequence from company as I did colony PCR using 16S primers. Now my question, can I make a phylogentic tree using that sequence?? If yes how? Explain. Thanks
Dear Aqleem,
your question is too general and you need to clarify the aim of your work, otherwise it's hard to help you. Depending on your interest and conditions, you have a lot of possibilities.
Just an example. If you found a specie never recognized before from a particular source, than you can use reference sequences commonly present in such source and make a phylogenetic tree of species present in your sample, showing their phylogenetic relationship, underlying the potential role of your specie in such environment.
Generally you choose the references to put in your tree depending on the aim of your research, so please explain deeply your question.
Regards
Of course you can,
You have just to align your sequence with other sequences of other strains (from Genbank) and build your tree using a software, I suggest MEGA.
First of all you have to retrieved your query sequence and then put it into BLAST search program. Subsequently, you have found some homogeneous sequences and select the most similar sequences on the basis of their maximum identity and query coverage. Then, you may build a phylogenetic tree based on your screened and query sequences by using MEGA Software.
I have used the 16S primers which are commonly used to identify bacteria. I sent the pcr product to company and they have sent me a sequence. Now I donot know how to make a phylogenetic tree of that sequence.
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