Do the BLAST scores have any relation between them?

Question

[Bahrani]

Is there any relation among the BLAST scores (E-value, similarity, identity, gap, bit score)? Is the e-value score for an alignment proportional to other scores, such as similarity score (i.e. the lower the e-value, the higher the similarity)?

Thank you!

Answer 1

[Philipp Bayer]

The e-value is calculated by taking the score and including the number of sequences in your database, i.e., "what is the probability that I get this score with this many sequences?"

See previous discussions, E-Value In Blast or Blast E Value Calculation

The score depends on the length of your alignment and your chosen substitution matrix, see these slides

Answer 2

[karl.stamm]

Yes they do.

https://en.wikipedia.org/wiki/BLAST