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Detect Stem-Loops With Dot-Plot

Hello Everyone,

I need an example of how to detect a stem-loop by using dot-plot, for that

  1. Find appropriate sequence(NCBI or any other genomic database)
  2. Use any dot-plot tool to identify the stem-loop regions (is there any pre-processing steps needed before for sequence)

If any one can provide a step by step example it would be very much appreciated

Thanks

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written by shamilsons • shamilsons

Why especially a dot plot, if there are much better tools?

• 0 views • link
written by Michael Dondrup Michael Dondrup

Hi Michael, which other tools I can use for finding stem-loops ?

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written by shamilsons • shamilsons

Everything that can find inverted repeats or palindromes, e.g.:

If you are looking for the minimum-free-energy structure of such sequence: RNAfold http://www.tbi.univie.ac.at/RNA/man/RNAfold.html

There is also this article but the software is unavailable:
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3400981/

• 0 views • link
written by Michael Dondrup Michael Dondrup

1 answer

Take a look at this website: http://ugene.unipro.ru/documentation/manual/sequence_view_extensions/dotplot/interpret_a_dotplot.html

In step 1, you can google for sequences with known stem-loop structures. Then, make a dotplot of sequence against itself (very nice dotplot is in Genious which has free trial, but there are many programs out there). Stem-loop regions will be visualized as inverted repeats.

• 144 views • link
written by Biomonika (Noolean) Biomonika (Noolean)

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