Table 1 Asymptotic runtimes. Asymptotic runtimes for the unfiltered cmsearch procedure and three filters, including our Sifter approach. R is the number of families in the current Rfam release. L is the target sequence length, N is the window size. |f| is the number of sequences in all families. r p is the remaining set of covariance models that have to be searched after the application of the filtering program p, r ≤ R.
From: Shape based indexing for faster search of RNA family databases
Program | Asymptotic runtime |
|---|---|
CM | O(R·L·N3) |
HMM | O(R·L·N2 + r HMM ·L·N3) |
BLAST | O(R·|f|·N + r BLAST ·L·N3) |
Sifter | O(N3 + r Sifter ·L·N3) |