Do the BLAST scores have any relation between them?
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!
2 answers
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
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Philipp Bayer
Yes they do.
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Ram
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karl.stamm
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