echlorop

 

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Function

Report presence of chloroplast transit peptides

Description

The ChloroP server predicts the presence of chloroplast transit peptides (cTP) in protein sequences and the location of potential cTP cleavage sites.

Usage

Here is a sample session with echlorop 


% echlorop 
Report presence of chloroplast transit peptides
Input (aligned) protein sequence set: test1.fsa
Output file [test1.echlorop]:

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

Example 2 


% echlorop 
Report presence of chloroplast transit peptides
Input (aligned) protein sequence set: test12.fsa
Output file [test12.echlorop]:

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

Command line arguments 

Report presence of chloroplast transit peptides
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     (Aligned) protein sequence set filename and
                                  optional format, or reference (input USA)
  [-outfile]           outfile    [*.echlorop] Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -full               boolean    [N] Show full output

   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 (Aligned) protein sequence set filename and optional format, or reference (input USA) Readable set of sequences Required
[-outfile]
(Parameter 2)		 outfile Output file name Output file <*>.echlorop
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-full boolean Show full output Boolean value Yes/No No
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

echlorop reads any normal sequence USAs.

Input files for usage example

File: test1.fsa

>P48786;       PATHOGENESIS-RELATED HOMEODOMAIN PROTEIN (PRHP).
MEEISDPKPNALEQVLPTVPNGKCTAPVQMESLAVDVQKVSGEAKVRICSCWCEIVRSPEDLTKLVPCNDFAEDIKLFDS
DPMQQEAESSIGIPLIPKQVTMSHNHDHESGSEMVSNEVMQENHVIATENTYQKSDFDRINMGQKETMPEEVIHKSFLES
STSSIDILLNNHNSYQSGLPPENAVTDCKQVQLGHRSDDAIKNSGLVELVIGQKNVAKSPSQLVETGKRGRGRPRKVQTG
LEQLVIGQKTAAKSSSQLGDTGKRSRGRPRKVQNSPTSFLENINMEQKETIPEQVTQNSILESLTIPTDNQSRTYNSDQS
ELPPENAAKNCNHAQFGHQSDDTTKISGFKELVIGQETVAKSPSQLVDAGKRGRGRPRKVQTGLEQLVPVQETAAKSSSQ
LGDTGKRSRGRPRKVQDSPTSLGGNVKVVPEKGKDSQELSVNSSRSLRSRSQEKSIEPDVNNIVADEGADREKPRKKRKK
RMEENRVDEFCRIRTHLRYLLHRIKYEKNFLDAYSGEGWKGQSLDKIKPEKELKRAKAEIFGRKLKIRDLFQRLDLARSE
GRLPEILFDSRGEIDSEDIFCAKCGSKDVTLSNDIILCDGACDRGFHQFCLDPPLLKEYIPPDDEGWLCPGCECKIDCIK
LLNDSQETNILLGDSWEKVFAEEAAAAASGKNLDDNSGLPSDDSEDDDYDPGGPDLDEKVQGDDSSTDESDYQSESDDMQ
VIRQKNSRGLPSDDSEDDEYDPSGLVTDQMYKDSSCSDFTSDSEDFTGVFDDYKDTGKAQGPLASTPDHVRNNEEGCGHP
EQGDTAPLYPRRQVESLDYKKLNDIEFSKMCDILDILSSQLDVIICTGNQEEYGNTSSDSSDEDYMVTSSPDKNNSDKEA
TAMERGRESGDLELDQKARESTHNRRYIKKFAVEGTDSFLSRSCEDSAAPVAGSKSTSKTLHGEHATQRLLQSFKENQYP
QRAVKESLAAELALSVRQVSNWFNNRRWSFRHSSRIGSDVAKFDSNDTPRQKSIDMSGPSLKSVLDSATYSEIEKKEQDT
ASLGLTEGCDRYMTLNMVADEGNVHTPCIAETREEKTEVGIKPQQNPL

Input files for usage example 2

File: test12.fsa

>P11043_it_is_a_very_very_long_name;       3-PHOSPHOSHIKIMATE 1-CARBOXYVINYLTRANSFERASE PRECURSOR (EC 2
MAQINNMAQGIQTLNPNSNFHKPQVPKSSSFLVFGSKKLKNSANSMLVLKKDSIFMQKFCSFRISASVATAQKPSEIVLQ
PIKEISGTVKLPGSKSLSNRILLLAALSEGTTVVDNLLSSDDIHYMLGALKTLGLHVEEDSANQRAVVEGCGGLFPVGKE
SKEEIQLFLGNAGTAMRPLTAAVTVAGGNSRYVLDGVPRMRERPISDLVDGLKQLGAEVDCFLGTKCPPVRIVSKGGLPG
GKVKLSGSISSQYLTALLMAAPLALGDVEIEIIDKLISVPYVEMTLKLMERFGISVEHSSSWDRFFVRGGQKYKSPGKAF
VEGDASSASYFLAGAAVTGGTITVEGCGTNSLQGDVKFAEVLEKMGAEVTWTENSVTVKGPPRSSSGRKHLRAIDVNMNK
MPDVAMTLAVVALYADGPTAIRDVASWRVKETERMIAICTELRKLGATVEEGPDYCIITPPEKLNVTDIDTYDDHRMAMA
FSLAACADVPVTINDPGCTRKTFPNYFDVLQQYSKH
>P07505;       SUPEROXIDE DISMUTASE, CHLOROPLAST PRECURSOR (CU-ZN) (EC 1.15
MAAHTILASAPSHTTFSLISPFSSTPTNALSSSLQSSSFNGLSFKLSPTTQSLSLSTSAASKPLTIVAATKKAVAVLKGT
SNVEGVVTLTQEDDGPTTVNVRISGLAPGKHGFHLHEFGDTTNGCMSTGPHFNPDKKTHGAPEDEVRHAGDLGNIVANTD
GVAEATIVDNQIPLTGPNSVVGRALVVHELEDDLGKGGHELSPTTGNAGGRLACGVVGLTPV
>P12360;       CHLOROPHYLL A-B BINDING PROTEIN OF LHCI TYPE I PRECURSOR (CA
MASNTLMSCGIPAVCPSFLSSTKSKFAAAMPVYVGATNFMSRFSMSADWMPGQPRPSYLDGSAPGDFGFDSLGLGEVPAN
LERYKESELIHCRWAMLAVPGIIVPEALGLGNWVKAQEWAAIPGGQATYLGQPVPWGTLPTILAIEFLAIAFVEHQRSME
KDSEKKKYPGGAFDPLGYSKDPAKFEELKVKEIKNGRLALLAIVGFCVQQSAYLGTGPLENLATHLADPWHNNIGDVIIP
KGIFPN
>P12352;       PHOTOSYSTEM I REACTION CENTRE SUBUNIT IV PRECURSOR (PHOTOSYS
MQALSSRVNIAAKPQRAQRLVVRAEEVKAAPKKEVGPKRGSLVKILRPESYWFNQVGKVVSVDQSGVRYPVVVRFENQNY
AGVTTNNYALDEVVAAK
>Q01289;       PROTOCHLOROPHYLLIDE REDUCTASE PRECURSOR (EC 1.3.1.33) (PCR) 
MALQTASMLPASFSIPKEGKIGASLKDSTLFGVSSLSDSLKGDFTSSALRCKELRQKVGAVRAETAAPATPAVNKSSSEG
KKTLRKGNVVITGASSGLGLATAKALAESGKWHVIMACRDYLKAARAAKSAGLAKENYTIMHLDLASLDSVRQFVDNFRR
SEMPLDVLINNAAVYFPTAKEPSFTADGFEISVGTNHLGHFLLSRLLLEDLKKSDYPSKRLIIVGSITGNTNTLAGNVPP
KANLGDLRGLAGGLTGLNSSAMIDGGDFDGAKAYKDSKVCNMLTMQEFHRRYHEETGITFASLYPGCIATTGLFREHIPL
FRTLFPPFQKYITKGYVSEEESGKRLAQVVSDPSLTKSGVYWSWNNASASFENQLSQEASDAEKARKVWEVSEKLVGLA 
>P08817;       ACYL CARRIER PROTEIN II PRECURSOR (ACP II).
MASAAASAVSFARPVKAICVNSVSFSALRKDNVSFRLQPVPQRFSVCCAAKKETVEKVCDIVKSQLALSDDTEVSGSSTF
ADLGADSLDTVEIVMGLEEAFGISVEESSAQTIATVEDAANLIDSLVGK
>P07263;       HISTIDYL-TRNA SYNTHETASE, MITOCHONDRIAL PRECURSOR (EC 6.1.1.
MLSRSLNKVVTSIKSSSIIRMSSATAAATSAPTANAANALKASKAPKKGKLQVSLKTPKGTKDWADSDMVIREAIFSTLS
GLFKKHGGVTIDTPVFELREILAGKYGEDSKLIYNLEDQGGELCSLRYDLTVPFARYVAMNNIQSIKRYHIAKVYRRDQP
AMTKGRMREFYQCDFDVAGTFESMVPDSECLSILVEGLTSLGIKDFKIKLNHRKILDGIFQIAGVKDEDVRKISSAVDKL
DKSPWEAVKKEMTEEKGQSEETADKIGEYVKLNGSLKEIHAVLSADANITSNEKAKQGLDDIATLMKYTEAFDIDSFISF
DLSLARGLDYYTGLIYEVVTSASAPPENASELKKKAKSAEDASEFVGVGSIAAGGRYDNLVNMFSEASGKKSTQIPCVGI
SFGVERIFSLIKQRINSSTTIKPTATQVFVMAFGGGKDWTGYLPERMKVTKQLWDAGIEAEYVYKAKANPRKQFDAAEKA
GCHIAVILGKEEYLEGKLRVKRLGQEFADDDGELVSAADIVPIVQEKLSQIHEDGLNEVTRLIKGL
>P07597;       NONSPECIFIC LIPID-TRANSFER PROTEIN 1 PRECURSOR (LTP 1) (PAPI
MARAQVLLMAAALVLMLTAAPRAAVALNCGQVDSKMKPCLTYVQGGPGPSGECCNGVRDLHNQAQSSGDRQTVCNCLKGI
ARGIHNLNLNNAASIPSKCNVNVPYTISPDIDCSRIY
>P48786;       PATHOGENESIS-RELATED HOMEODOMAIN PROTEIN (PRHP).
MEEISDPKPNALEQVLPTVPNGKCTAPVQMESLAVDVQKVSGEAKVRICSCWCEIVRSPEDLTKLVPCNDFAEDIKLFDS
DPMQQEAESSIGIPLIPKQVTMSHNHDHESGSEMVSNEVMQENHVIATENTYQKSDFDRINMGQKETMPEEVIHKSFLES
STSSIDILLNNHNSYQSGLPPENAVTDCKQVQLGHRSDDAIKNSGLVELVIGQKNVAKSPSQLVETGKRGRGRPRKVQTG
LEQLVIGQKTAAKSSSQLGDTGKRSRGRPRKVQNSPTSFLENINMEQKETIPEQVTQNSILESLTIPTDNQSRTYNSDQS
ELPPENAAKNCNHAQFGHQSDDTTKISGFKELVIGQETVAKSPSQLVDAGKRGRGRPRKVQTGLEQLVPVQETAAKSSSQ
LGDTGKRSRGRPRKVQDSPTSLGGNVKVVPEKGKDSQELSVNSSRSLRSRSQEKSIEPDVNNIVADEGADREKPRKKRKK
RMEENRVDEFCRIRTHLRYLLHRIKYEKNFLDAYSGEGWKGQSLDKIKPEKELKRAKAEIFGRKLKIRDLFQRLDLARSE
GRLPEILFDSRGEIDSEDIFCAKCGSKDVTLSNDIILCDGACDRGFHQFCLDPPLLKEYIPPDDEGWLCPGCECKIDCIK
LLNDSQETNILLGDSWEKVFAEEAAAAASGKNLDDNSGLPSDDSEDDDYDPGGPDLDEKVQGDDSSTDESDYQSESDDMQ
VIRQKNSRGLPSDDSEDDEYDPSGLVTDQMYKDSSCSDFTSDSEDFTGVFDDYKDTGKAQGPLASTPDHVRNNEEGCGHP
EQGDTAPLYPRRQVESLDYKKLNDIEFSKMCDILDILSSQLDVIICTGNQEEYGNTSSDSSDEDYMVTSSPDKNNSDKEA
TAMERGRESGDLELDQKARESTHNRRYIKKFAVEGTDSFLSRSCEDSAAPVAGSKSTSKTLHGEHATQRLLQSFKENQYP
QRAVKESLAAELALSVRQVSNWFNNRRWSFRHSSRIGSDVAKFDSNDTPRQKSIDMSGPSLKSVLDSATYSEIEKKEQDT
ASLGLTEGCDRYMTLNMVADEGNVHTPCIAETREEKTEVGIKPQQNPL
>Q01238;       MAJOR BASIC NUCLEAR PROTEIN 2 (P14 PROTEIN ALPHA CHAIN).
MKAMKATKKAMTKTGLAEALAPKPSSARRIAPPSSRAWPPSAQEVKKTGKLIIPGLVMVKTRKKPATKAGKREMFGKVVL
VKAQPAKTVVKAYPVKALKDNF
>P35334;       POLYGALACTURONASE INHIBITOR PRECURSOR (POLYGALACTURONASE-INH
MTQFNIPVTMSSSLSIILVILVSLRTALSELCNPQDKQALLQIKKDLGNPTTLSSWLPTTDCCNRTWLGVLCDTDTQTYR
VNNLDLSGHNLPKPYPIPSSLANLPYLNFLYIGGINNLVGPIPPAIAKLTQLHYLYITHTNVSGAIPDFLSQIKTLVTLD
FSYNALSGTLPPSISSLPNLGGITFDGNRISGAIPDSYGSFSKLFTAMTISRNRLTGKIPPTFANLNLAFVDLSRNMLEG
DASVLFGSDKNTKKIHLAKNSLAFDLGKVGLSKNLNGLDLRNNRIYGTLPQGLTQLKFLQSLNVSFNNLCGEIPQGGNLK
RFDVSSYANNKCLCGSPLPSCT
>P13086;       SUCCINYL-COA LIGASE (GDP-FORMING), ALPHA-CHAIN PRECURSOR (EC
MVSGSSGLAAARLLSRTFLLQQNGIRHGSYTASRKNIYIDKNTKVICQGFTGKQGTFHSQQALEYGTKLVGGTTPGKGGK
KHLGLPVFNTVKEAKEKTGATASVIYVPPPFAAAAINEAIDAEIPLVVCITEGIPQQDMLRVKHKLTRQGKTRLIGPNCP
GIINPGECKIGIMPGHIHKKGRIGIVSRSGTLTYEAVHQTTQVGLGQSLCIGIGGDPFNGTNFIDCLDVFLKDPATEGIV
LIGEIGGHAEENAAEFLKEHNSGPKAKPVVSFIAGITAPPGRRMGHAGAIIAGGKGGAKEKISALQSAGVIVSMSPAQLG
TCMYKEFEKRKML

Output file format

Output files for usage example

File: test1.echlorop


### chlorop v1.1 prediction results ###########################
Number of query sequences: 1

Name                  Length       Score  cTP       CS-    cTP-
                                                  score  length
---------------------------------------------------------------
P48786;                 1088	   0.434   -	 -0.663	    28
---------------------------------------------------------------

Output files for usage example 2

File: test12.echlorop


### chlorop v1.1 prediction results ###########################
Number of query sequences: 12

Name                  Length       Score  cTP       CS-    cTP-
                                                  score  length
---------------------------------------------------------------
P11043_it_is_a_very_     516	   0.580   Y	  6.765	    65
P07505;                  222	   0.596   Y	 11.122	    67
P12360;                  246	   0.566   Y	  1.302	    42
P12352;                   97	   0.470   -	 13.692	    23
Q01289;                  399	   0.532   Y	 10.699	    62
P08817;                  129	   0.559   Y	 12.650	    47
P07263;                  546	   0.534   Y	  4.495	    41
P07597;                  117	   0.465   -	  4.575	    22
P48786;                 1088	   0.434   -	 -0.663	    28
Q01238;                  102	   0.533   Y	  8.666	    41
P35334;                  342	   0.465   -	  4.342	    71
P13086;                  333	   0.460   -	  0.747	    48
---------------------------------------------------------------

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program name Description
elipop Predict lipoproteins
esignalp Report protein signal cleavage sites
etmhmm Reports transmembrane helices
sigcleave Report on signal cleavage sites in a protein sequence
siggenlig Generate ligand-binding signatures from a CON file
sigscan Generate hits (DHF file) from a signature search
tmap Predict and plot transmembrane segments in protein sequences
topo Draw an image of a transmembrane protein

Author(s)

This program is an EMBOSS wrapper for a program written by the CBS group http://www.cbs.dtu.dk/index.shtml

The original CBS group application must be licensed and installed to use this wrapper.

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) 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