reverse complementary matches in two sequences.

Question

[HK]

Hey All,

I have a two DNA strings, and want to check if they reverse complementary to each other (or part of that).

: https://ibb.co/e5pOKn

As shown in this imagine, i have the sequence of the encircled part (grey) and want to find the highly reverse complimentary (as shown in the red dotted line), As you can see only part of the sequence a reverse complimentary was found. I was wondering if anyone knows any computational tool/package how to do this.

Answer 1

[btf]

The simplest tool to look for this is DNA dotplots, where direct repeats show up as parallel lines whereas inverted repeats (reverse complimentarity) show up as lines at 90 degree angels to each other.

http://resources.qiagenbioinformatics.com/manuals/clcmainworkbench/780/index.php?manual=Examples_interpretations_dot_plots.html

If you are looking for very small regions it can be difficult to find them especially if the self-complimentarity is not 100% perfect. Most RNA or DNA strings will be predicted to for complex secondary structures when using a program like RNAfold, due to random bits of self comlimentarity so it is not easy to sort out truly significant or important RNA secondary structures (such as ribosomal RNA stem-loops, tRNA stem-loops, TAR and PSI elements in HIV genome, etc) from random ones. I am not an expert in mRNA splicing but my understanding is that there is some influence of self complimentarity near the splice sites but it is quite small and weak and may be difficult to detect. Actually, I think my recollection of complimentarity in introns was for self-splicing introns in prokaryotes and not for eukaryotic introns which use a spliceosome.