                                  echlorop



Wiki

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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


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-CARBOXYVINYLTRAN
SFERASE 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 (c) 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
