Skip to main content

Table 4 GENPPI execution line with parameters to generate interaction networks keeps fixed expansions for conserved neighbourhoods and variations controlling the number of phylogenetic profile interactions

From: GENPPI: standalone software for creating protein interaction networks from genomes

Id

Parameters

f1

genppi -expt fixed -w1 10 -cw1 3 -ppiterlimit 1000000 -ppdifftolerated 3 -ppaadifflimit 0

f2

genppi -expt fixed -w1 10 -cw1 4 -trim 20000

f3

genppi -expt fixed -w1 10 -cw1 1 -ppiterlimit 500000

f4

genppi -expt fixed -w1 10 -cw1 1 -ppcomplete -aadifflimit 0 -aachecklimit 24

d5

genppi -expt dynamic -ws 3 -ppcomplete -ppdifftolerated 1 -pphistofilter

  1. We omitted the folder parameter (-dir) for not contributing changes in the nodes or edges’ volume resulting in the networks. Execution d5 is a dynamic expansion for the conserved neighbourhood. d5 has no counterpart results of a fixed retraction. d5 was maintained in this table solely to group the documentation on the exploited commands
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us