Question: Gettin Consensus From Multiple Whole Genomes
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gravatar for nilaylale88
3.4 years ago by
nilaylale880 wrote:

Hello guys, newbie here.

I have 15 microRNA sequences from rats. I used Velvet and SSPACE to assemble the genomes. Assembeled genomes are 8-9 Mbp, what i am targeting is apply MSA and get consensus within these 15 genomes and then do the genome annotation on that consensus seq. I tried, Clustalx, Kalign, Muscle etc. no result. Lately I have tried Mauve but i could not get any consensus from Mauve. Can anyone help me with this?

ADD COMMENTlink modified 3.3 years ago by Biostar ♦♦ 20 • written 3.4 years ago by nilaylale880
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Hi nilaylale. Your questions is full of contradictions and claims that do not make sense, please fix them before someone can attempt to give an answer. Just to point out a few:

15 microRNA sequences from rats (what for, unrelated to rest of Q?)

Assembeled genomes are 8-9 Mbp (that's not even close to the size of the rat genome (~2.7Gb), if that is the real size of your assembly, there is no need to continue with your analysis at all)

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Michael Dondrup47k

Sorry, fresh graduate here. Thanks for quick reply. There are 15 microRNA sequences from rats which are given heroin and another 15 microRNA sequences that are control group. What i was told is, assemble those and get a consensus from each group. After that compare those 2 consensus and do the annotation. The unassembled trimmed seq range from 22Mbp to 40Mbp. Am I doing this all wrong? I thought the size is very small too, but since its microRNA, i thought its ok.

ADD REPLYlink written 3.4 years ago by nilaylale880
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Checkout https://en.wikipedia.org/wiki/MicroRNA and https://en.wikipedia.org/wiki/Genome MicroRNAs != genome

"I have ... miRNA sequences", given in which form, from which experiment? If you are given mature miRNA sequences you don't need to assemble them. Using velvet and sspace on miRNA data is not a valid approach anyway.

In this context, your question makes little sense, nor does the task description. You should clarify the misunderstanding with your supervisor first.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Michael Dondrup47k

BINF 6203: Genome Comparison with Mauve

http://genomeintelligence.org/?p=1157

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by natasha.sernova3.7k
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