In brouwern/blaststats: What the Package Does (Replication of Altschul and Gish 1996 Local Alignment Statistics)

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(blaststats)

Add to compbio for all?

Logging splits up multiplication into addition. So, log(m*n) is the same as log(m) + log(n)

You can check this

m<-10
n<-11
log(m*n)

log(m)+log(n)

log(m*n) == log(m)+log(n)

Exponentiation undoes logs

exp(log(m*n))
m*n

The key equation in BLAST's E values is

u = ln(Kmn)/lambda

This can be changed to

[ln(K) + ln(mn)]/lambda

We can check this

K <- 1
m <- 10
n <- 11
lambda <- 110

log(K*m*n)/lambda

(log(K) + log(m*n))/lambda

log(K*m*n)/lambda == (log(K) + log(m*n))/lambda

brouwern/blaststats documentation built on Dec. 19, 2021, 11:47 a.m.