Table 1. HSP determination and filtering

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