EMBASSY: IPRSCAn: eiprscan

eiprscan

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Function

Motif detection

Description

Algorithm

Usage

Here is a sample session with eiprscan

% eiprscan -nocrc -goterms -iprlookup Motif detection Input 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-20100115-12345678

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

Command line arguments

Motif detection
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     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
   -sformat1           string     Input sequence format
   -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 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

-sformat1
-sformat_sequence string Input sequence format Any string

-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

RS16_ECOLI	F94D07049A6D489D	82	BlastProDom	PD003791	RS16_BUCAI_P57474;	9	77	1e-19	T	12-Jan-2010	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	Coil	coil	coiled-coil	225	246	NA	?	12-Jan-2010	NULL	NULL
RS16_ECOLI	F94D07049A6D489D	82	Gene3D	G3DSA:3.30.1320.10	no description	1	77	1.7e-25	T	12-Jan-2010	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	Gene3D	G3DSA:2.40.50.140	no description	3	57	4.5e-10	T	12-Jan-2010	IPR012340	Nucleic acid-binding, OB-fold	
Q9RHD9	D44DAE8C544CB7C1	267	Gene3D	G3DSA:2.40.50.140	no description	67	144	1.3e-16	T	12-Jan-2010	IPR012340	Nucleic acid-binding, OB-fold	
Q9RHD9	D44DAE8C544CB7C1	267	Gene3D	G3DSA:2.40.50.140	no description	156	230	9.2e-17	T	12-Jan-2010	IPR012340	Nucleic acid-binding, OB-fold	
Y902_MYCTU	CD84A335CCFFE6D7	446	Gene3D	G3DSA:3.30.565.10	no description	301	443	6.3e-25	T	12-Jan-2010	IPR003594	ATP-binding region, ATPase-like	Molecular Function: ATP binding (GO:0005524)
Y902_MYCTU	CD84A335CCFFE6D7	446	HMMPanther	PTHR23283:SF23	SENSORY TRANSDUCTION HISTIDINE KINASE (BACTERIAL SENSOR PROTEIN)	6	57	1.9e-48	T	12-Jan-2010	NULL	NULL	
Y902_MYCTU	CD84A335CCFFE6D7	446	HMMPanther	PTHR23283:SF23	SENSORY TRANSDUCTION HISTIDINE KINASE (BACTERIAL SENSOR PROTEIN)	151	443	1.9e-48	T	12-Jan-2010	NULL	NULL	
Y902_MYCTU	CD84A335CCFFE6D7	446	HMMPanther	PTHR23283	SENSOR HISTIDINE KINASE-RELATED	6	57	1.9e-48	T	12-Jan-2010	NULL	NULL	
Y902_MYCTU	CD84A335CCFFE6D7	446	HMMPanther	PTHR23283	SENSOR HISTIDINE KINASE-RELATED	151	443	1.9e-48	T	12-Jan-2010	NULL	NULL	
RS16_ECOLI	F94D07049A6D489D	82	HMMPanther	PTHR12919	30S RIBOSOMAL PROTEIN S16	1	78	4.2e-36	T	12-Jan-2010	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	PTHR23270	PROGRAMMED CELL DEATH PROTEIN 11 (PRE-RRNA PROCESSING PROTEIN RRP5)	72	239	2.6e-09	T	12-Jan-2010	NULL	NULL	
RS16_ECOLI	F94D07049A6D489D	82	HMMPfam	PF00886	Ribosomal_S16	8	68	1.5e-35	T	12-Jan-2010	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	1	55	1.9e-08	T	12-Jan-2010	IPR003029	S1, RNA binding	Molecular Function: RNA binding (GO:0003723)
Q9RHD9	D44DAE8C544CB7C1	267	HMMPfam	PF00575	S1	68	142	2.2e-21	T	12-Jan-2010	IPR003029	S1, RNA binding	Molecular Function: RNA binding (GO:0003723)
Q9RHD9	D44DAE8C544CB7C1	267	HMMPfam	PF00575	S1	155	228	9.7e-22	T	12-Jan-2010	IPR003029	S1, RNA binding	Molecular Function: RNA binding (GO:0003723)
Y902_MYCTU	CD84A335CCFFE6D7	446	HMMPfam	PF00672	HAMP	151	219	4.7e-11	T	12-Jan-2010	IPR003660	Signal transduction histidine kinase, HAMP region	Molecular Function: signal transducer activity (GO:0004871), Biological Process: signal transduction (GO:0007165), Cellular Component: membrane (GO:0016020)
Y902_MYCTU	CD84A335CCFFE6D7	446	HMMPfam	PF00512	HisKA	230	296	1.3e-13	T	12-Jan-2010	IPR003661	Signal transduction histidine kinase, subgroup 1, dimerisation and phosphoacceptor region	Molecular Function: two-component sensor activity (GO:0000155), Biological Process: signal transduction (GO:0007165), Cellular Component: membrane (GO:0016020)
Y902_MYCTU	CD84A335CCFFE6D7	446	HMMPfam	PF02518	HATPase_c	338	445	3.4e-29	T	12-Jan-2010	IPR003594	ATP-binding region, ATPase-like	Molecular Function: ATP binding (GO:0005524)
Q9RHD9	D44DAE8C544CB7C1	267	HMMSmart	SM00316	no description	3	55	1.2e-06	T	12-Jan-2010	IPR003029	S1, RNA binding	Molecular Function: RNA binding (GO:0003723)
Q9RHD9	D44DAE8C544CB7C1	267	HMMSmart	SM00316	no description	70	142	1.4e-19	T	12-Jan-2010	IPR003029	S1, RNA binding	Molecular Function: RNA binding (GO:0003723)
Q9RHD9	D44DAE8C544CB7C1	267	HMMSmart	SM00316	no description	157	228	2.6e-21	T	12-Jan-2010	IPR003029	S1, RNA binding	Molecular Function: RNA binding (GO:0003723)
Y902_MYCTU	CD84A335CCFFE6D7	446	HMMSmart	SM00304	no description	170	222	3.1e-06	T	12-Jan-2010	IPR003660	Signal transduction histidine kinase, HAMP region	Molecular Function: signal transducer activity (GO:0004871), Biological Process: signal transduction (GO:0007165), Cellular Component: membrane (GO:0016020)
Y902_MYCTU	CD84A335CCFFE6D7	446	HMMSmart	SM00388	no description	230	296	2.4e-12	T	12-Jan-2010	IPR003661	Signal transduction histidine kinase, subgroup 1, dimerisation and phosphoacceptor region	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	12-Jan-2010	IPR003594	ATP-binding region, ATPase-like	Molecular Function: ATP binding (GO:0005524)
RS16_ECOLI	F94D07049A6D489D	82	HMMTigr	TIGR00002	S16: ribosomal protein S16	2	81	1.8e-32	T	12-Jan-2010	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	12-Jan-2010	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	12-Jan-2010	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	12-Jan-2010	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	12-Jan-2010	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	12-Jan-2010	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	12-Jan-2010	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	12-Jan-2010	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	ScanRegExp	PS00732	RIBOSOMAL_S16	2	11	8e-5	T	12-Jan-2010	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	ProfileScan	PS50126	S1	1	55	14.869	T	12-Jan-2010	IPR003029	S1, RNA binding	Molecular Function: RNA binding (GO:0003723)
Q9RHD9	D44DAE8C544CB7C1	267	ProfileScan	PS50126	S1	72	142	20.809	T	12-Jan-2010	IPR003029	S1, RNA binding	Molecular Function: RNA binding (GO:0003723)
Q9RHD9	D44DAE8C544CB7C1	267	ProfileScan	PS50126	S1	159	228	22.541	T	12-Jan-2010	IPR003029	S1, RNA binding	Molecular Function: RNA binding (GO:0003723)
Y902_MYCTU	CD84A335CCFFE6D7	446	ProfileScan	PS50885	HAMP	170	222	7.777	T	12-Jan-2010	IPR003660	Signal transduction histidine kinase, HAMP region	Molecular Function: signal transducer activity (GO:0004871), Biological Process: signal transduction (GO:0007165), Cellular Component: membrane (GO:0016020)
Y902_MYCTU	CD84A335CCFFE6D7	446	ProfileScan	PS50109	HIS_KIN	237	446	34.449	T	12-Jan-2010	IPR005467	Signal transduction histidine kinase, core	Molecular Function: two-component sensor activity (GO:0000155), Molecular Function: protein histidine kinase activity (GO:0004673), Biological Process: signal transduction (GO:0007165), Biological Process: peptidyl-histidine phosphorylation (GO:0018106)
RS16_ECOLI	F94D07049A6D489D	82	superfamily	SSF54565	Ribosomal protein S16	1	79	3.1e-27	T	12-Jan-2010	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	superfamily	SSF50249	Nucleic acid-binding proteins	67	220	7.6e-41	T	12-Jan-2010	IPR016027	Nucleic acid-binding, OB-fold-like	
Q9RHD9	D44DAE8C544CB7C1	267	superfamily	SSF50249	Nucleic acid-binding proteins	3	61	1.4e-14	T	12-Jan-2010	IPR016027	Nucleic acid-binding, OB-fold-like	
Y902_MYCTU	CD84A335CCFFE6D7	446	superfamily	SSF55874	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	303	444	8e-31	T	12-Jan-2010	IPR003594	ATP-binding region, ATPase-like	Molecular Function: ATP binding (GO:0005524)
Y902_MYCTU	CD84A335CCFFE6D7	446	superfamily	SSF47384	Homodimeric domain of signal transducing histidine kinase	220	292	4.8e-12	T	12-Jan-2010	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	?	12-Jan-2010	NULL	NULL
Q9RHD9	D44DAE8C544CB7C1	267	Seg	seg	seg	84	98	NA	?	12-Jan-2010	NULL	NULL
Q9RHD9	D44DAE8C544CB7C1	267	Seg	seg	seg	222	237	NA	?	12-Jan-2010	NULL	NULL
Y902_MYCTU	CD84A335CCFFE6D7	446	Seg	seg	seg	44	55	NA	?	12-Jan-2010	NULL	NULL
Y902_MYCTU	CD84A335CCFFE6D7	446	Seg	seg	seg	108	120	NA	?	12-Jan-2010	NULL	NULL
Y902_MYCTU	CD84A335CCFFE6D7	446	Seg	seg	seg	160	173	NA	?	12-Jan-2010	NULL	NULL
Y902_MYCTU	CD84A335CCFFE6D7	446	Seg	seg	seg	308	319	NA	?	12-Jan-2010	NULL	NULL
Y902_MYCTU	CD84A335CCFFE6D7	446	Seg	seg	seg	400	424	NA	?	12-Jan-2010	NULL	NULL

Data files

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

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Program name	Description
antigenic	Finds antigenic sites in proteins
digest	Reports on protein proteolytic enzyme or reagent cleavage sites
echlorop	Reports presence of chloroplast transit peptides
elipop	Prediction of lipoproteins
emast	Motif detection
ememe	Multiple EM for Motif Elicitation
ememetext	Multiple EM for Motif Elicitation. Text file only
enetnglyc	Reports N-glycosylation sites in human proteins
enetoglyc	Reports mucin type GalNAc O-glycosylation sites in mammalian proteins
enetphos	Reports ser, thr and tyr phosphorylation sites in eukaryotic proteins
epestfind	Finds PEST motifs as potential proteolytic cleavage sites
eprop	Reports propeptide cleavage sites in proteins
esignalp	Reports protein signal cleavage sites
etmhmm	Reports transmembrane helices
eyinoyang	Reports O-(beta)-GlcNAc attachment sites
fuzzpro	Search for patterns in protein sequences
fuzztran	Search for patterns in protein sequences (translated)
helixturnhelix	Identify nucleic acid-binding motifs in protein sequences
oddcomp	Identify proteins with specified sequence word composition
omeme	Motif detection
patmatdb	Searches protein sequences with a sequence motif
patmatmotifs	Scan a protein sequence with motifs from the PROSITE database
pepcoil	Predicts coiled coil regions in protein sequences
preg	Regular expression search of protein sequence(s)
pscan	Scans protein sequence(s) with fingerprints from the PRINTS database
sigcleave	Reports 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.

Although we take every care to ensure that the results of the EMBOSS version are identical to those from the original package, we recommend that you check your inputs give the same results in both versions before publication.

Please report all bugs in the EMBOSS version to the EMBOSS bug team, not to the original author.

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