EMBASSY: IPRSCAn: eiprscan

eiprscan

Wiki

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Function

Motif detection

Description

InterProScan is a tool that combines different protein signature recognition methods native to the InterPro member databases into one resource with look up of corresponding InterPro and GO annotation.

Algorithm

Usage

Here is a sample session with eiprscan

% eiprscan -nocrc -goterms -iprlookup Motif detection Input protein sequence set: iprtest.seq Applications to use all : all blastprodom : blastprodom coils : coils gene3d : gene3d hmmpanther : hmmpanther hmmpir : hmmpir hmmpfam : hmmpfam hmmsmart : hmmsmart hmmtigr : hmmtigr fprintscan : fprintscan scanregexp : scanregexp profilescan : profilescan superfamily : superfamily seg : seg signalp : signalp tmhmm : tmhmm Application(s) to use [all]: Output Formats raw : Raw txt : Text html : Html xml : Xml ebixml : EBIxml gff : GFF Format to use [xml]: raw EIPRSCAN program output file [iprtest.eiprscan]: SUBMITTED-iprscan-20110715-12345678

Go to the input files for this example
Go to the output files for this example

Command line arguments

Motif detection
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     Protein sequence set filename and optional
                                  format, or reference (input USA)
   -appl               menu       [all] Application(s) to use (Values: all
                                  (all); blastprodom (blastprodom); coils
                                  (coils); gene3d (gene3d); hmmpanther
                                  (hmmpanther); hmmpir (hmmpir); hmmpfam
                                  (hmmpfam); hmmsmart (hmmsmart); hmmtigr
                                  (hmmtigr); fprintscan (fprintscan);
                                  scanregexp (scanregexp); profilescan
                                  (profilescan); superfamily (superfamily);
                                  seg (seg); signalp (signalp); tmhmm (tmhmm))
   -format             menu       [xml] Format to use (Values: raw (Raw); txt
                                  (Text); html (Html); xml (Xml); ebixml
                                  (EBIxml); gff (GFF))
  [-outfile]           outfile    [*.eiprscan] EIPRSCAN program output file

   Additional (Optional) qualifiers (* if not always prompted):
   -email              string     Submitter email address (Any string)
   -trtable            menu       [0] Genetic codes used for translation
                                  (Values: 0 (Standard); 1 (Standard (with
                                  alternative initiation codons)); 2
                                  (Vertebrate Mitochondrial); 3 (Yeast
                                  Mitochondrial); 4 (Mold, Protozoan,
                                  Coelenterate Mitochondrial and
                                  Mycoplasma/Spiroplasma); 5 (Invertebrate
                                  Mitochondrial); 6 (Ciliate Macronuclear and
                                  Dasycladacean); 9 (Echinoderm
                                  Mitochondrial); 10 (Euplotid Nuclear); 11
                                  (Bacterial); 12 (Alternative Yeast Nuclear);
                                  13 (Ascidian Mitochondrial); 14 (Flatworm
                                  Mitochondrial); 15 (Blepharisma
                                  Macronuclear); 16 (Chlorophycean
                                  Mitochondrial); 21 (Trematode
                                  Mitochondrial); 22 (Scenedesmus obliquus);
                                  23 (Thraustochytrium Mitochondrial))
   -trlen              integer    [1] Minimum size of Open Reading Frames
                                  (ORFs) in the translations. (Integer 1 or
                                  more)
   -iprlookup          boolean    [N] Turn on InterPro lookup for results
*  -goterms            boolean    [N] Show GO terms in InterPro lookup
   -[no]crc            boolean    [Y] Perform CRC64 check
   -altjobs            boolean    [N] Launch jobs alternately (chunk after
                                  chunk)

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default

Standard (Mandatory) qualifiers

[-sequence]
(Parameter 1) seqset Protein sequence set filename and optional format, or reference (input USA) Readable set of sequences Required

-appl list Application(s) to use
all (all)
blastprodom (blastprodom)
coils (coils)
gene3d (gene3d)
hmmpanther (hmmpanther)
hmmpir (hmmpir)
hmmpfam (hmmpfam)
hmmsmart (hmmsmart)
hmmtigr (hmmtigr)
fprintscan (fprintscan)
scanregexp (scanregexp)
profilescan (profilescan)
superfamily (superfamily)
seg (seg)
signalp (signalp)
tmhmm (tmhmm)
all

-format list Format to use
raw (Raw)
txt (Text)
html (Html)
xml (Xml)
ebixml (EBIxml)
gff (GFF)
xml

[-outfile]
(Parameter 2) outfile EIPRSCAN program output file Output file <*>.eiprscan

Additional (Optional) qualifiers

-email string Submitter email address Any string

-trtable list Genetic codes used for translation
0 (Standard)
1 (Standard (with alternative initiation codons))
2 (Vertebrate Mitochondrial)
3 (Yeast Mitochondrial)
4 (Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma)
5 (Invertebrate Mitochondrial)
6 (Ciliate Macronuclear and Dasycladacean)
9 (Echinoderm Mitochondrial)
10 (Euplotid Nuclear)
11 (Bacterial)
12 (Alternative Yeast Nuclear)
13 (Ascidian Mitochondrial)
14 (Flatworm Mitochondrial)
15 (Blepharisma Macronuclear)
16 (Chlorophycean Mitochondrial)
21 (Trematode Mitochondrial)
22 (Scenedesmus obliquus)
23 (Thraustochytrium Mitochondrial)
0

-trlen integer Minimum size of Open Reading Frames (ORFs) in the translations. Integer 1 or more 1

-iprlookup boolean Turn on InterPro lookup for results Boolean value Yes/No No

-goterms boolean Show GO terms in InterPro lookup Boolean value Yes/No No

-[no]crc boolean Perform CRC64 check Boolean value Yes/No Yes

-altjobs boolean Launch jobs alternately (chunk after chunk) Boolean value Yes/No No

Advanced (Unprompted) qualifiers

(none)

Associated qualifiers

"-sequence" associated seqset qualifiers

-sbegin1
-sbegin_sequence integer Start of each sequence to be used Any integer value 0

-send1
-send_sequence integer End of each sequence to be used Any integer value 0

-sreverse1
-sreverse_sequence boolean Reverse (if DNA) Boolean value Yes/No N

-sask1
-sask_sequence boolean Ask for begin/end/reverse Boolean value Yes/No N

-snucleotide1
-snucleotide_sequence boolean Sequence is nucleotide Boolean value Yes/No N

-sprotein1
-sprotein_sequence boolean Sequence is protein Boolean value Yes/No N

-slower1
-slower_sequence boolean Make lower case Boolean value Yes/No N

-supper1
-supper_sequence boolean Make upper case Boolean value Yes/No N

-scircular1
-scircular_sequence boolean Sequence is circular Boolean value Yes/No N

-squick1
-squick_sequence boolean Read id and sequence only Boolean value Yes/No N

-sformat1
-sformat_sequence string Input sequence format Any string

-iquery1
-iquery_sequence string Input query fields or ID list Any string

-ioffset1
-ioffset_sequence integer Input start position offset Any integer value 0

-sdbname1
-sdbname_sequence string Database name Any string

-sid1
-sid_sequence string Entryname Any string

-ufo1
-ufo_sequence string UFO features Any string

-fformat1
-fformat_sequence string Features format Any string

-fopenfile1
-fopenfile_sequence string Features file name Any string

"-outfile" associated outfile qualifiers

-odirectory2
-odirectory_outfile string Output directory Any string

General qualifiers

-auto boolean Turn off prompts Boolean value Yes/No N

-stdout boolean Write first file to standard output Boolean value Yes/No N

-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N

-options boolean Prompt for standard and additional values Boolean value Yes/No N

-debug boolean Write debug output to program.dbg Boolean value Yes/No N

-verbose boolean Report some/full command line options Boolean value Yes/No Y

-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N

-warning boolean Report warnings Boolean value Yes/No Y

-error boolean Report errors Boolean value Yes/No Y

-fatal boolean Report fatal errors Boolean value Yes/No Y

-die boolean Report dying program messages Boolean value Yes/No Y

-version boolean Report version number and exit Boolean value Yes/No N

Input file format

eiprscan reads any normal sequence USAs.

Input files for usage example

File: iprtest.seq

>RS16_ECOLI
MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHW
VGQGATISDRVAALIKEVNKAA
>Q9RHD9
XPKLEEGVEGLVHVSEMDWTNKNIHPSKVVQVGDEVEVQVLDIDEERRRISLGIKQCKSN
PWEDFSSQFNKGDRISGSIKSITDFGIFIGLDGGIDGLVHLSDISWNEVGEEAVRRFKKG
DELETVILSVDPERERISLGIKQLEDDPFSNYASLHEKGSIVRGTVKEVDAKGAVISLGD
DIEGILKASEISRDRVEDARNVLKEGEEVEAKIISIDRKSRVISLSVKSKDVDDEKDAMK
ELRKQEVESAGPTTIGDLIRAQMENQG
>Y902_MYCTU Q10560 PROBABLE SENSOR-LIKE HISTIDINE KINASE RV0902C (EC 2.7.3.-).
MNILSRIFARTPSLRTRVVVATAIGAAIPVLIVGTVVWVGITNDRKERLDRRLDEAAGFA
IPFVPRGLDEIPRSPNDQDALITVRRGNVIKSNSDITLPKLQDDYADTYVRGVRYRVRTV
EIPGPEPTSVAVGATYDATVAETNNLHRRVLLICTFAIGAAAVFAWLLAAFAVRPFKQLA
EQTRSIDAGDEAPRVEVHGASEAIEIAEAMRGMLQRIWNEQNRTKEALASARDFAAVSSH
ELRTPLTAMRTNLEVLSTLDLPDDQRKEVLNDVIRTQSRIEATLSALERLAQGELSTSDD
HVPVDITDLLDRAAHDAARIYPDLDVSLVPSPTCIIVGLPAGLRLAVDNAIANAVKHGGA
TLVQLSAVSSRAGVEIAIDDNGSGVPEGERQVVFERFSRGSTASHSGSGLGLALVAQQAQ
LHGGTASLENSPLGGARLVLRLPGPS

Output file format

eiprscan outputs a file in a format selected from the commandline options

Output files for usage example

File: iprtest.eiprscan

Q9RHD9	D44DAE8C544CB7C1	267	Coil	coil	coiled-coil	225	246	NA	?	13-Dec-2011	NULL	NULL
Q9RHD9	D44DAE8C544CB7C1	267	Gene3D	G3DSA:2.40.50.140	no description	4	65	2.2e-21	T	13-Dec-2011	IPR012340	Nucleic acid-binding, OB-fold	
Q9RHD9	D44DAE8C544CB7C1	267	Gene3D	G3DSA:2.40.50.140	no description	66	146	5.8e-25	T	13-Dec-2011	IPR012340	Nucleic acid-binding, OB-fold	
Q9RHD9	D44DAE8C544CB7C1	267	Gene3D	G3DSA:2.40.50.140	no description	147	228	1.6e-21	T	13-Dec-2011	IPR012340	Nucleic acid-binding, OB-fold	
RS16_ECOLI	F94D07049A6D489D	82	Gene3D	G3DSA:3.30.1320.10	no description	1	79	1.1e-31	T	13-Dec-2011	IPR023803	Ribosomal protein S16 domain	
Y902_MYCTU	CD84A335CCFFE6D7	446	Gene3D	G3DSA:1.10.287.240	no description	222	287	2.4e-08	T	13-Dec-2011	NULL	NULL	
Y902_MYCTU	CD84A335CCFFE6D7	446	Gene3D	G3DSA:3.30.565.10	no description	302	444	5.2e-26	T	13-Dec-2011	IPR003594	ATPase-like, ATP-binding domain	Molecular Function: ATP binding (GO:0005524)
Y902_MYCTU	CD84A335CCFFE6D7	446	HMMPanther	PTHR24423	FAMILY NOT NAMED	27	443	6.7e-36	T	13-Dec-2011	NULL	NULL	
RS16_ECOLI	F94D07049A6D489D	82	HMMPanther	PTHR12919:SF12	SUBFAMILY NOT NAMED	1	77	5.2e-50	T	13-Dec-2011	NULL	NULL	
RS16_ECOLI	F94D07049A6D489D	82	HMMPanther	PTHR12919	FAMILY NOT NAMED	1	77	5.2e-50	T	13-Dec-2011	IPR000307	Ribosomal protein S16	Molecular Function: structural constituent of ribosome (GO:0003735), Cellular Component: intracellular (GO:0005622), Cellular Component: ribosome (GO:0005840), Biological Process: translation (GO:0006412)
Q9RHD9	D44DAE8C544CB7C1	267	HMMPanther	PTHR10724	S1 RNA-BINDING DOMAIN-CONTAINING PROTEIN 1	4	156	2.4e-69	T	13-Dec-2011	NULL	NULL	
RS16_ECOLI	F94D07049A6D489D	82	HMMPfam	PF00886	Ribosomal_S16	8	68	8.7e-26	T	13-Dec-2011	IPR000307	Ribosomal protein S16	Molecular Function: structural constituent of ribosome (GO:0003735), Cellular Component: intracellular (GO:0005622), Cellular Component: ribosome (GO:0005840), Biological Process: translation (GO:0006412)
Q9RHD9	D44DAE8C544CB7C1	267	HMMPfam	PF00575	S1	4	55	1.5e-14	T	13-Dec-2011	IPR003029	Ribosomal protein S1, RNA-binding domain	Molecular Function: RNA binding (GO:0003723)
Q9RHD9	D44DAE8C544CB7C1	267	HMMPfam	PF00575	S1	69	142	1.8e-18	T	13-Dec-2011	IPR003029	Ribosomal protein S1, RNA-binding domain	Molecular Function: RNA binding (GO:0003723)
Q9RHD9	D44DAE8C544CB7C1	267	HMMPfam	PF00575	S1	156	228	4.7e-19	T	13-Dec-2011	IPR003029	Ribosomal protein S1, RNA-binding domain	Molecular Function: RNA binding (GO:0003723)
Y902_MYCTU	CD84A335CCFFE6D7	446	HMMPfam	PF02518	HATPase_c	340	443	4.6e-18	T	13-Dec-2011	IPR003594	ATPase-like, ATP-binding domain	Molecular Function: ATP binding (GO:0005524)
Y902_MYCTU	CD84A335CCFFE6D7	446	HMMPfam	PF00512	HisKA	232	293	3.2e-11	T	13-Dec-2011	IPR003661	Signal transduction histidine kinase, subgroup 1, dimerisation/phosphoacceptor domain	Molecular Function: two-component sensor activity (GO:0000155), Biological Process: signal transduction (GO:0007165), Cellular Component: membrane (GO:0016020)
Y902_MYCTU	CD84A335CCFFE6D7	446	HMMPfam	PF00672	HAMP	151	217	2.1e-10	T	13-Dec-2011	IPR003660	HAMP linker domain	Molecular Function: signal transducer activity (GO:0004871), Biological Process: signal transduction (GO:0007165), Cellular Component: integral to membrane (GO:0016021)
Q9RHD9	D44DAE8C544CB7C1	267	HMMSmart	SM00316	no description	3	55	1.2e-06	T	13-Dec-2011	IPR022967	RNA-binding domain, S1	
Q9RHD9	D44DAE8C544CB7C1	267	HMMSmart	SM00316	no description	70	142	1.4e-19	T	13-Dec-2011	IPR022967	RNA-binding domain, S1	
Q9RHD9	D44DAE8C544CB7C1	267	HMMSmart	SM00316	no description	157	228	2.6e-21	T	13-Dec-2011	IPR022967	RNA-binding domain, S1	
Y902_MYCTU	CD84A335CCFFE6D7	446	HMMSmart	SM00304	no description	170	222	3.1e-06	T	13-Dec-2011	IPR003660	HAMP linker domain	Molecular Function: signal transducer activity (GO:0004871), Biological Process: signal transduction (GO:0007165), Cellular Component: integral to membrane (GO:0016021)
Y902_MYCTU	CD84A335CCFFE6D7	446	HMMSmart	SM00388	no description	230	296	2.4e-12	T	13-Dec-2011	IPR003661	Signal transduction histidine kinase, subgroup 1, dimerisation/phosphoacceptor domain	Molecular Function: two-component sensor activity (GO:0000155), Biological Process: signal transduction (GO:0007165), Cellular Component: membrane (GO:0016020)
Y902_MYCTU	CD84A335CCFFE6D7	446	HMMSmart	SM00387	no description	338	446	5e-24	T	13-Dec-2011	IPR003594	ATPase-like, ATP-binding domain	Molecular Function: ATP binding (GO:0005524)
RS16_ECOLI	F94D07049A6D489D	82	HMMTigr	TIGR00002	S16: ribosomal protein S16	2	78	1.1e-28	T	13-Dec-2011	IPR000307	Ribosomal protein S16	Molecular Function: structural constituent of ribosome (GO:0003735), Cellular Component: intracellular (GO:0005622), Cellular Component: ribosome (GO:0005840), Biological Process: translation (GO:0006412)
Q9RHD9	D44DAE8C544CB7C1	267	FPrintScan	PR00681	RIBOSOMALS1	6	27	7.9e-17	T	13-Dec-2011	IPR000110	Ribosomal protein S1	Molecular Function: RNA binding (GO:0003723), Molecular Function: structural constituent of ribosome (GO:0003735), Cellular Component: ribosome (GO:0005840), Biological Process: translation (GO:0006412)
Q9RHD9	D44DAE8C544CB7C1	267	FPrintScan	PR00681	RIBOSOMALS1	85	104	7.9e-17	T	13-Dec-2011	IPR000110	Ribosomal protein S1	Molecular Function: RNA binding (GO:0003723), Molecular Function: structural constituent of ribosome (GO:0003735), Cellular Component: ribosome (GO:0005840), Biological Process: translation (GO:0006412)
Q9RHD9	D44DAE8C544CB7C1	267	FPrintScan	PR00681	RIBOSOMALS1	125	143	7.9e-17	T	13-Dec-2011	IPR000110	Ribosomal protein S1	Molecular Function: RNA binding (GO:0003723), Molecular Function: structural constituent of ribosome (GO:0003735), Cellular Component: ribosome (GO:0005840), Biological Process: translation (GO:0006412)
Y902_MYCTU	CD84A335CCFFE6D7	446	FPrintScan	PR00344	BCTRLSENSOR	374	388	1.1e-11	T	13-Dec-2011	IPR004358	Signal transduction histidine kinase-related protein, C-terminal	Biological Process: phosphorylation (GO:0016310), Molecular Function: transferase activity, transferring phosphorus-containing groups (GO:0016772)
Y902_MYCTU	CD84A335CCFFE6D7	446	FPrintScan	PR00344	BCTRLSENSOR	392	402	1.1e-11	T	13-Dec-2011	IPR004358	Signal transduction histidine kinase-related protein, C-terminal	Biological Process: phosphorylation (GO:0016310), Molecular Function: transferase activity, transferring phosphorus-containing groups (GO:0016772)
Y902_MYCTU	CD84A335CCFFE6D7	446	FPrintScan	PR00344	BCTRLSENSOR	406	424	1.1e-11	T	13-Dec-2011	IPR004358	Signal transduction histidine kinase-related protein, C-terminal	Biological Process: phosphorylation (GO:0016310), Molecular Function: transferase activity, transferring phosphorus-containing groups (GO:0016772)
Y902_MYCTU	CD84A335CCFFE6D7	446	FPrintScan	PR00344	BCTRLSENSOR	430	443	1.1e-11	T	13-Dec-2011	IPR004358	Signal transduction histidine kinase-related protein, C-terminal	Biological Process: phosphorylation (GO:0016310), Molecular Function: transferase activity, transferring phosphorus-containing groups (GO:0016772)
RS16_ECOLI	F94D07049A6D489D	82	superfamily	SSF54565	Ribosomal protein S16	1	79	5.3e-27	T	13-Dec-2011	IPR023803	Ribosomal protein S16 domain	
Q9RHD9	D44DAE8C544CB7C1	267	superfamily	SSF50249	Nucleic acid-binding proteins	137	254	1.9e-29	T	13-Dec-2011	IPR016027	Nucleic acid-binding, OB-fold-like	
Q9RHD9	D44DAE8C544CB7C1	267	superfamily	SSF50249	Nucleic acid-binding proteins	58	143	8.5e-23	T	13-Dec-2011	IPR016027	Nucleic acid-binding, OB-fold-like	
Q9RHD9	D44DAE8C544CB7C1	267	superfamily	SSF50249	Nucleic acid-binding proteins	3	68	2.5e-15	T	13-Dec-2011	IPR016027	Nucleic acid-binding, OB-fold-like	
Y902_MYCTU	CD84A335CCFFE6D7	446	superfamily	SSF55874	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	299	446	2.1e-33	T	13-Dec-2011	IPR003594	ATPase-like, ATP-binding domain	Molecular Function: ATP binding (GO:0005524)
Y902_MYCTU	CD84A335CCFFE6D7	446	superfamily	SSF47384	Homodimeric domain of signal transducing histidine kinase	212	298	5.5e-12	T	13-Dec-2011	IPR009082	Signal transduction histidine kinase, homodimeric	Molecular Function: signal transducer activity (GO:0004871), Biological Process: signal transduction (GO:0007165)
Q9RHD9	D44DAE8C544CB7C1	267	Seg	seg	seg	29	40	NA	?	13-Dec-2011	NULL	NULL
Q9RHD9	D44DAE8C544CB7C1	267	Seg	seg	seg	84	98	NA	?	13-Dec-2011	NULL	NULL
Q9RHD9	D44DAE8C544CB7C1	267	Seg	seg	seg	222	237	NA	?	13-Dec-2011	NULL	NULL
Y902_MYCTU	CD84A335CCFFE6D7	446	Seg	seg	seg	44	55	NA	?	13-Dec-2011	NULL	NULL
Y902_MYCTU	CD84A335CCFFE6D7	446	Seg	seg	seg	108	120	NA	?	13-Dec-2011	NULL	NULL
Y902_MYCTU	CD84A335CCFFE6D7	446	Seg	seg	seg	160	173	NA	?	13-Dec-2011	NULL	NULL
Y902_MYCTU	CD84A335CCFFE6D7	446	Seg	seg	seg	308	319	NA	?	13-Dec-2011	NULL	NULL
Y902_MYCTU	CD84A335CCFFE6D7	446	Seg	seg	seg	400	424	NA	?	13-Dec-2011	NULL	NULL

Data files

None other rthan the databases configured for the native iprscan application.

Notes

None.

References

See Zdobnov E.M. and Apweiler R. "InterProScan - an integration platform for the signature-recognition methods in InterPro" Bioinformatics, 2001, 17(9): p. 847-8.

See InterPro documentation available at: http://www.ebi.ac.uk/interpro/

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Program name	Description
antigenic	Find antigenic sites in proteins
elipop	Predict lipoproteins
emast	Motif detection
ememe	Multiple EM for motif elicitation
ememetext	Multiple EM for motif elicitation, text file only
epestfind	Find PEST motifs as potential proteolytic cleavage sites
fuzzpro	Search for patterns in protein sequences
fuzztran	Search for patterns in protein sequences (translated)
omeme	Motif detection
patmatdb	Search protein sequences with a sequence motif
patmatmotifs	Scan a protein sequence with motifs from the PROSITE database
preg	Regular expression search of protein sequence(s)
pscan	Scan protein sequence(s) with fingerprints from the PRINTS database
sigcleave	Report on signal cleavage sites in a protein sequence

Author(s)

This program is an EMBOSS wrapper for the InterProSCAN application "iprscan"

The original iprscan application must be installed and configured to use this wrapper.

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None

Wiki

Function

Description

Algorithm

Usage

Command line arguments

Input file format

Input files for usage example

File: iprtest.seq

Output file format

Output files for usage example

File: iprtest.eiprscan

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments