How lambda parameter works in BLAST?
How lambda parameter works in BLAST? It is calculated using the following equation (https://doi.org/10.1073/pnas.87.6.2264):
Scoring matrix is calculated using:
While bit score using:
My questions:
- To calculate lambda we need scoring matrix, and to calculate scoring matrix we need lambda. How does it work?
- To calculate scoring matrix we divide logarithm by lambda, and to calculate bit score we multiply raw alignment score by lambda. Therefore, lambda parameter has no effect. Is it correct?
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Found something that might be related to the values of lambda and K, perhaps you could check this?
https://bioinformatics.stackexchange.com/questions/5145/calculating-bit-score-how-do-you-find-lambda-and-k
From the post: