secondary structure comparison - how to approach this? / tools?

Question

[Xylanaser]

I want to compare two secondary structures of aligned proteins. I do not know exactly how to do it well.

Example:

EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHHHHHHHHHCHCCTHHEEEETTTEEECTTTEEECTTTEEC

EEEHHHHHHHTTTTTTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCCCCCCCEEEEEEEEEEEEEE

Example of matching:

EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHHHHHHHHHCHCCTHHEEEETTTEEECTTTEEECTTTEEC
|||        |||||| |||                    |||||||||     ||||||      |   |||    ||
EEEHHHHHHHTTTTTTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHEEEECCCCCCCCCCEEEEEEEEEE

Hypothetically: 50% aligned - > score 0.5 - > thats scoring is wrong:

EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHHHHHHHHHCHCCTHHEEEETTTEEECTTTEEECTTTEEC
||||||||||||||||||||||||||||||||||||||||||
EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHEEEEEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHH

This case will have similar score...

This is a puzzle for me, I don't know how to approach it technically.

Answer 1

[Mensur Dlakic]

There used to be a tool for that, but it is currently unavailable:

https://academic.oup.com/bioinformatics/article/21/3/393/237965

There is a tool that calculates secondary structure overlap (SOV), but it doesn't do any (re)alignments. Instead, it is meant to compare real and predicted secondary structures. On your first example, the SOV score is 20.5 (see the results here).

http://proteinmodel.org/AS2TS/SOV/sov.html

https://github.com/nanjiangshu/calSOV

[Xylanaser]

Thank you, it solves my problem. Best wishes