                                  echlorop



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Function

   Reports 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
Reports presence of chloroplast transit peptides
Input (aligned) 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
Reports presence of chloroplast transit peptides
Input (aligned) 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

Reports presence of chloroplast transit peptides
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     (Aligned) 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
   -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


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
   antigenic        Finds antigenic sites in proteins
   digest           Reports on protein proteolytic enzyme or reagent cleavage sites
   eiprscan         Motif detection
   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 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.

   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
