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!
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hnp21 •
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:
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?
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.
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% similarity is meant for protein blast (which uses substitution matrix) not for nucleotide blast