BLAST: Identity % and Similarity %
1
4
Entering edit mode
8.5 years ago
hnp21 ▴ 50

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!

blast • 51k views
ADD COMMENT
4
Entering edit mode

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

ADD REPLY
2
Entering edit mode
ADD COMMENT
0
Entering edit mode

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?

ADD REPLY
1
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 1235 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6