Welcome to InterProScan-5.24-63.0
usage: java -XX:+UseParallelGC -XX:ParallelGCThreads=2 -XX:+AggressiveOpts
-XX:+UseFastAccessorMethods -Xms128M -Xmx2048M -jar
interproscan-5.jar
Please give us your feedback by sending an email to
interhelp@ebi.ac.uk
-appl,--applications Optional, comma separated list
of analyses. If this option
is not set, ALL analyses will
be run.
-b,--output-file-base Optional, base output filename
(relative or absolute path).
Note that this option, the
--output-dir (-d) option and
the --outfile (-o) option are
mutually exclusive. The
appropriate file extension for
the output format(s) will be
appended automatically. By
default the input file
path/name will be used.
-cpu,--cpu Optional, number of cores for
inteproscan.
-d,--output-dir Optional, output directory.
Note that this option, the
--outfile (-o) option and the
--output-file-base (-b) option
are mutually exclusive. The
output filename(s) are the
same as the input filename,
with the appropriate file
extension(s) for the output
format(s) appended
automatically .
-dp,--disable-precalc Optional. Disables use of the
precalculated match lookup
service. All match
calculations will be run
locally.
-dra,--disable-residue-annot Optional, excludes sites from
the XML, JSON output
-f,--formats Optional, case-insensitive,
comma separated list of output
formats. Supported formats are
TSV, XML, JSON, GFF3, HTML and
SVG. Default for protein
sequences are TSV, XML and
GFF3, or for nucleotide
sequences GFF3 and XML.
-goterms,--goterms Optional, switch on lookup of
corresponding Gene Ontology
annotation (IMPLIES -iprlookup
option)
-help,--help Optional, display help
information
-i,--input Optional, path to fasta file
that should be loaded on
Master startup. Alternatively,
in CONVERT mode, the
InterProScan 5 XML file to
convert.
-iprlookup,--iprlookup Also include lookup of
corresponding InterPro
annotation in the TSV and GFF3
output formats.
-ms,--minsize Optional, minimum nucleotide
size of ORF to report. Will
only be considered if n is
specified as a sequence type.
Please be aware of the fact
that if you specify a too
short value it might be that
the analysis takes a very long
time!
-o,--outfile Optional explicit output file
name (relative or absolute
path). Note that this option,
the --output-dir (-d) option
and the --output-file-base
(-b) option are mutually
exclusive. If this option is
given, you MUST specify a
single output format using the
-f option. The output file
name will not be modified.
Note that specifying an output
file name using this option
OVERWRITES ANY EXISTING FILE.
-pa,--pathways Optional, switch on lookup of
corresponding Pathway
annotation (IMPLIES -iprlookup
option)
-t,--seqtype Optional, the type of the
input sequences (dna/rna (n)
or protein (p)). The default
sequence type is protein.
-T,--tempdir Optional, specify temporary
file directory (relative or
absolute path). The default
location is temp/.
-version,--version Optional, display version
number
Copyright © EMBL European Bioinformatics Institute, Hinxton, Cambridge,
UK. (http://www.ebi.ac.uk) The InterProScan software itself is provided
under the Apache License, Version 2.0
(http://www.apache.org/licenses/LICENSE-2.0.html). Third party components
(e.g. member database binaries and models) are subject to separate
licensing - please see the individual member database websites for
details.
Available analyses:
TIGRFAM (15.0) : TIGRFAMs are protein families based on Hidden Markov Models or HMMs
SFLD (2) : SFLDs are protein families based on Hidden Markov Models or HMMs
Phobius (1.01) : A combined transmembrane topology and signal peptide predictor
SignalP_GRAM_NEGATIVE (4.1) : SignalP (organism type gram-negative prokaryotes) predicts the presence and location of signal peptide cleavage sites in amino acid sequences for gram-negative prokaryotes.
SUPERFAMILY (1.75) : SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.
PANTHER (11.1) : The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
Gene3D (4.1.0) : Structural assignment for whole genes and genomes using the CATH domain structure database
Hamap (201701.18) : High-quality Automated and Manual Annotation of Microbial Proteomes
ProSiteProfiles (20.132) : PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them
Coils (2.2.1) : Prediction of Coiled Coil Regions in Proteins
SMART (7.1) : SMART allows the identification and analysis of domain architectures based on Hidden Markov Models or HMMs
CDD (3.14) : Prediction of CDD domains in Proteins
PRINTS (42.0) : A fingerprint is a group of conserved motifs used to characterise a protein family
ProSitePatterns (20.132) : PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them
SignalP_EUK (4.1) : SignalP (organism type eukaryotes) predicts the presence and location of signal peptide cleavage sites in amino acid sequences for eukaryotes.
Pfam (31.0) : A large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)
ProDom (2006.1) : ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.
MobiDBLite (1.0) : Prediction of disordered domains Regions in Proteins
SignalP_GRAM_POSITIVE (4.1) : SignalP (organism type gram-positive prokaryotes) predicts the presence and location of signal peptide cleavage sites in amino acid sequences for gram-positive prokaryotes.
PIRSF (3.02) : The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships.
TMHMM (2.0c) : Prediction of transmembrane helices in proteins
