BLAST: Identity % and Similarity %

Question

[hnp21]

Hello Biostars! Could you please tell me how to get both Identity % and similarity % of a blast (nucleotide) output? Web-BLAST just gives the identity %. Appreciate your input!

[Prasad]

% similarity is meant for protein blast (which uses substitution matrix) not for nucleotide blast

Answer 1

[natasha.sernova]

This is BLAST glossary, find there 'alignment' and both definitions:

http://www.ncbi.nlm.nih.gov/books/NBK62051/

See this biostars.org-post:

Is there a way to find the percent similarity just like percent identity in BLAST?

Below you will find the calculation itself:

https://www.quora.com/What-is-the-difference-between-the-percentage-similarity-and-the-percentage-identity-of-two-sequences

[hnp21]

Thank you so much for the reply.

What I wanted to know was, how to get both Identity % and similarity % in a blast output. When I use web-BLAST, I just get Identity % but not the similarity %. Is there any command which could be used to get both Identity % and similarity % during BLAST analysis?

[natasha.sernova]

As to similarity. See again this link:

Is there a way to find the percent similarity just like percent identity in BLAST?

They mentioned a very useful presentation. Look at it.

http://homepages.ulb.ac.be/~dgonze/TEACHING/stat_scores.pdf

Especially at the 7th slide from this presentation, @5heikki suggested it. There you will find what you need:

'Positives' ratio equals to similarity % in protein Blast output.

The ratio is determined as Positive score in the substitution matrix.

But it works only for proteins (aas) and useless for nucleotides as @Prasad said above.