BLAST Score vs E-value in BioPython

Question

[dlawre14]

When I use the following in BioPython

result.alignments[0].hsps[0].score

What value is this? Is it the alignment score based on gap and mismatch penalties or the e-value? When using the above, is a larger number or a smaller number better?

[karl.stamm]

"better" implies you're trying to do something with the values.

The values are defined by the BLAST method, and are not specific to BioPython. Research what BLAST does and you'll see what each value means.

[dlawre14]

I know from the blast side the difference between BLAST score and e-value, I was unclear on my call which value BioPython is calling hsps.score, is that equivalent to BLAST score? I am doing a machine learning project on protein function prediction and one of my methods is to align the subject against a database of proteins and then return predicted functionality as the function of the closest aligned protein in the database.

Answer 1

[DG]

The documentation for BioPython has this information well defined. For HSPs: http://biopython.org/DIST/docs/api/Bio.Blast.Record.HSP-class.html hsp.score is the score, hsp.expect is the expect value.

As karl.stamm pointed out in his comments, deciding which to use and how to interpret it depends on what you are trying to do and these are well defined by BLAST as to what they mean.

[dlawre14]

Ah thank you. I read the documentation and must have missed the hsp.expect choice for hsp records. Boy do I feel dumb.