Algorithm | WU BLASTa | NCBI BLASTb | BLATc | MUMmerd | BLASTZe |
---|---|---|---|---|---|
Run time | Very high [M] | Low [M] | High [M] | Very low [M] | Moderate [M] |
Memory consumption and output size | High [M] | Moderate [M] | Moderate [M] | Very low [M] | Low [M] |
Typical effect on correlation with DDH values | decrease [M] | increase [M] | increase [M] | moderate increase [M] | decrease [M] |
Seed parameter | W= | -W | -tileSize | -l | T=0 W= |
Typical effect on runtime, RAM usage and file size | higher → speedup smaller output files [E] | higher → speedup smaller output files [E] | higher → speedup; lower → significant increase of memory consumption [M] | higher → speedup smaller output files [M] | higher → speedup smaller output files [E] |
Typical effect on correlation with DDH values | N/A | N/A | lower → decrease of correlation [M] | higher → increase of correlation [M] | N/A |
Identity parameter | score based, i.e., identical to initial word length | score based, i.e., identical to initial word length | -minIdentity | 100% (fixed) | score based, i.e., identical to initial word length |
Typical effect on runtime, RAM usage and file size | N/A | N/A | insignificant [M] | (none) | N/A |
Typical effect on correlation with DDH values | N/A | N/A | lower → increase of correlation [M] | N/A | N/A |
Measure of HSP quality used for filtering | e-value | e-value | substitution score | (makes no sense) | substitution score |
Typical effect on subsequent runtime and RAM usage | insignificant [E] | insignificant [E] | lower → small increase of runtime and memory consumption [M] | (none) | lower → small increase of runtime and memory consumption [M] |
Typical effect on correlation with DDH values | insignificant [E] | insignificant [E] | lower → small increase of correlation | N/A | higher → slight increase of correlation |