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How to predict complementary nucleotide sequence?

Hi, I want to predict complementary between mRNAs. How can I do that? Is there any option available with BLASTn?

Thank you

alignment blast assembly genome
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updated by biobiu biobiu • written by Neu • Neu

Hello, Why is your question taged with R?

Anyway, I am not sure of what means predict complimentary between mRNAs. Does it mean that you look in a a pool of mRNA sequences for some that could partially make a ddRNA?

Well, for this, it seems the best start would be on a local blast install: -create a local blast DB out of your mRNA sequences -blast your mRNA against that DB -look for plus/minus match you'll get the sequences of mRNA binding to other mRNA

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written by gbl1 gbl1

Are there any opensource datasets which contain the DNA of an individual and the diseases asssociated with this DNA

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written by sabithabca123 • sabithabca123

2 answers 

 echo "$1" | tr "[ATGCYRSWKMBDHVatgcyrswkmbdhv]" "[TACGRYSWMKVHDBtacgryswmkvhdb]" | rev
• 1 views • link
written by 5heikki 5heikki

It really depends on what you are looking for (what is the minimal length of the complementary regions? should they match perfectly? etc.). In example, miRNA should have (almost) exact match in the seed region but does not require any match outside the seed. Generally speaking, in order to find complementary sequences between two RNA molecules I would look for plus minus blast alignments.

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written by biobiu biobiu

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