Practical value of bits and SW-score in KEGG
SW score is most likely the Smith-Waterman score, basically the sum of all reward+penalities of the alignment.
The bitscore is also an alignment score, invented with BLAST I believe that
The bit score, S’, is derived from the raw alignment score, S, taking the statistical properties of the scoring system into account. Because bit scores are normalized with respect to the scoring system, they can be used to compare alignment scores from different searches.
Since alignment algorithms maximize score, these scores are the sole reasons of why one alignment is preferred versus the other. The practical value is in assessing how similar the scores may be when the alignment themselves may be very different.
If we see two radically different alignments that score very similarly we ought to be more cautious.
In general bitscores are used to filter data and reduce the number of hits to more manageable number.
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