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. rp is the remaining set of covariance models that have to be searched after the application of the filtering program p, r ≤ R. |
|
|
Program |
Asymptotic runtime |
|
|
|
|
CM |
O(R·L·N3) |
|
HMM |
O(R·L·N2 + rHMM·L·N3) |
|
BLAST |
O(R·|f|·N + rBLAST·L·N3) |
|
Sifter |
O(N3 + rSifter·L·N3) |
|
|
|
|
Janssen et al. BMC Bioinformatics 2008 9:131 doi:10.1186/1471-2105-9-131 |
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