Blast K and Lambda

Question

[Haifeng]

Hello, I have a question about Blast parameter.

In Blast search results, for different queries the K and Lambda value is different for Ungapped search. For gapped search , they are the same

However, for other software, for example, UBlast, and RAPsearch2, they set the K and Lambda as a fixed parameter?

Do this matter the results?

Thanks in advance

Answer 1

[Istvan Albert]

The K and Lambda parameters govern the way Bitscores and E-values are computed.

Here is a more detailed explanation

But as for the answer, yes indeed they do matter but maybe not in the way you expect. Their choice will affect the way the scores are computed and the actual magnitude of them. But in general I would not worry too much about them.

In my opinion these scores and the underlying mathematics are more of an illusion when it comes to biological interpretation - they should be used to weed out obviously redundant hits but beyond that don't have that much use.

[Haifeng]

Thanks a lot. That's really helpful.