I have some proteins with blast homologs, and I am trying to get a quantitative measure of the representativeness of each match. As I understand, everyone normally compares blast alignments using bit scores, as these are database-size independent. However (please correct me if I'm wrong) bit-scores only describe the quality of the HSP itself, not how representative that HSP/bit score is of it's parent protein.
Would I be barking up the wrong tree if I DIYed a score for comparison? One of the main reasons I'm asking is I'm not particularly hot on BLAST statistics (so this may all be unnecessary) and I know making up your own stats can be a bad idea.
My score would be something like:
(bitscore * perc_coverage)/log (evalue)
This would hopefully approximate to:
(quality of HSP * HSP representativeness of protein) / reliability of HSP quality
NB - I would take the log to stop differences in E-value massively biasing the final score.
Thanks for reading!
Ahh perfect thanks for the reply - I thought I might be getting ahead of myself, so glad I sanity checked this!
Out of interest/for my own learning, do you mean (i) longer queries, or (ii) longer query subsequences contained in a given HSP here? I'm guessing the second based on this , which says:
(assuming by 'alignment' they mean HSPs)
My point was that bit-scores are biased by query length (your first choice), but that also extends to the expected alignment length (your second choice).