This is a test version of Biostars. For the public version, visit https://www.biostars.org.
secondary structure comparison - how to approach this? / tools?

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.

secondarystructure python structure protein
• 1,463 views • link
updated by Mensur Dlakic Mensur Dlakic • written by Xylanaser Xylanaser

1 answer

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

• 0 views • link
written by Mensur Dlakic Mensur Dlakic

Thank you, it solves my problem. Best wishes

• 0 views • link
written by Xylanaser Xylanaser

Log in to answer this question.

More posts like this