Detect Stem-Loops With Dot-Plot

Question

[shamilsons]

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

[Michael]

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

[shamilsons]

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

[Michael]

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

• http://emboss.sourceforge.net/apps/cvs/emboss/apps/palindrome.html
• http://emboss.sourceforge.net/apps/cvs/emboss/apps/einverted.html

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/

Answer 1

[Biomonika (Noolean)]

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.