|
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
|
