ORFfold parameters#
Mandatory
-faa
fasta file containing the amino acid sequences to treat
-options
indicates which properties are to be calculated. H for
estimating the fold potential with HCA, I for the estimation of the disorder
propensity with IUPred and T for the aggregation propensity with Tango. Combinations
of letters are accepted if the user wants to calculate several properties at the
same time (-options HIT will estimate the three properties)(default: H).
Optional
-h, --help
shows this help message and exits
-gff
gff annotation file. The ID (i.e. annotation) of the
sequences given in the input FASTA file sequence must be identical to the ID label
in the gff file (column #3). ORFold generates as many gff
files as studied properties (fold potential, disorder and/or aggregation
propensities), each containing for the sequences provided in the input fasta file,
their corresponding property values (fold potential, disorder or aggregation
propensities). The values are stored in the column #9 of the output gff files
that can be subsequently uploaded on a genome viewer (see here
examples on the use of this option).
-keep
ORFold uses IUPred and Tango for the prediction of the disorder
and aggregation propensities. For storage reasons, by default, ORFold does not save the output
files of these two methods. Nevertheless, the user can keep the Tango
output files through the option -keep.
-keep T will save Tango output files in the TANGO directory.
-N
Working with large genomes can eventually generate quite big files. For
that reason, ORFold has also the option to generate a sample of the initial dataset
and perform the calculation only on this specific subset of the population. This
option enables the user to indicate the number of randomly selected sequences to be treated by ORFold.