Practical value of bits and SW-score in KEGG

Question

[George X.]

Hello,

Can someone explain to me the practical value of bits and SW-score in KEGG? What does it actually mean for my sequence? The image below shows paralogs table as shown in the base what is the practical value of these parameters there? Thank you!

Answer 1

[Istvan Albert]

SW score is most likely the Smith-Waterman score, basically the sum of all reward+penalities of the alignment.

• https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm

The bitscore is also an alignment score, invented with BLAST I believe that

• https://www.ncbi.nlm.nih.gov/books/NBK62051/

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.

[George X.]

Thank you very much :)