Compare and Analyze char patterns

Hi... i'm trying to compare and analyze different miRNAs for a project

I have a cell matrix with the Dot-Bracket notation for the miRNAs and I'm trying to compare and possibly identify patterns in two different groups in order to study the secondary structure...

Since it's not an amminoacidic or nucleotidic sequence normal alignment tools avaible in matlab are useless... what should I use?

[Sean de Wolski]

Can you show us a small example? Data /operation /expected output?

[Giulio]

A='.(((...........((((((.((((..((((((((..((((((( (((((((...)))))))....))))))).))))))))..)))).))))))((.....)).))).'

B='.......(((((.((((....(((.(((((...(((.(....).)))(.(.((((..(((....)))..)))).).).))))).)))...)))).)))))'

I need to find if there are similarities in the patterns (like if this motif is present --> .(....). <-- or other motifs.

Translating in letters it's like to find if in a sentence there are some letters, subwords that repeats into different strings

A='hELLO world matlab' B='yELLOw bELLOw'

I know it's a complicate request and probably there is no easy way but maybe someone can help me...

[Sean de Wolski]

Well it'll be doable with regular expressions but it'll be a fun challenge. There might even be somethng for this in the Bioinformatics Toolbox.

[Ingrid Tigges]

This thread on MATLAB answers might be helpful http://www.mathworks.com/matlabcentral/newsreader/view_thread/281532

[Giulio]

Thanks so much!

[Ingrid Tigges]

You are welcome :-)