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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
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. 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
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
(Aligned) sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required |
| [-outfile] (Parameter 2) |
Output file name | Output file | <*>.echlorop |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -full | Show full output | Boolean value Yes/No | No |
>P48786; PATHOGENESIS-RELATED HOMEODOMAIN PROTEIN (PRHP). MEEISDPKPNALEQVLPTVPNGKCTAPVQMESLAVDVQKVSGEAKVRICSCWCEIVRSPEDLTKLVPCNDFAEDIKLFDS DPMQQEAESSIGIPLIPKQVTMSHNHDHESGSEMVSNEVMQENHVIATENTYQKSDFDRINMGQKETMPEEVIHKSFLES STSSIDILLNNHNSYQSGLPPENAVTDCKQVQLGHRSDDAIKNSGLVELVIGQKNVAKSPSQLVETGKRGRGRPRKVQTG LEQLVIGQKTAAKSSSQLGDTGKRSRGRPRKVQNSPTSFLENINMEQKETIPEQVTQNSILESLTIPTDNQSRTYNSDQS ELPPENAAKNCNHAQFGHQSDDTTKISGFKELVIGQETVAKSPSQLVDAGKRGRGRPRKVQTGLEQLVPVQETAAKSSSQ LGDTGKRSRGRPRKVQDSPTSLGGNVKVVPEKGKDSQELSVNSSRSLRSRSQEKSIEPDVNNIVADEGADREKPRKKRKK RMEENRVDEFCRIRTHLRYLLHRIKYEKNFLDAYSGEGWKGQSLDKIKPEKELKRAKAEIFGRKLKIRDLFQRLDLARSE GRLPEILFDSRGEIDSEDIFCAKCGSKDVTLSNDIILCDGACDRGFHQFCLDPPLLKEYIPPDDEGWLCPGCECKIDCIK LLNDSQETNILLGDSWEKVFAEEAAAAASGKNLDDNSGLPSDDSEDDDYDPGGPDLDEKVQGDDSSTDESDYQSESDDMQ VIRQKNSRGLPSDDSEDDEYDPSGLVTDQMYKDSSCSDFTSDSEDFTGVFDDYKDTGKAQGPLASTPDHVRNNEEGCGHP EQGDTAPLYPRRQVESLDYKKLNDIEFSKMCDILDILSSQLDVIICTGNQEEYGNTSSDSSDEDYMVTSSPDKNNSDKEA TAMERGRESGDLELDQKARESTHNRRYIKKFAVEGTDSFLSRSCEDSAAPVAGSKSTSKTLHGEHATQRLLQSFKENQYP QRAVKESLAAELALSVRQVSNWFNNRRWSFRHSSRIGSDVAKFDSNDTPRQKSIDMSGPSLKSVLDSATYSEIEKKEQDT ASLGLTEGCDRYMTLNMVADEGNVHTPCIAETREEKTEVGIKPQQNPL |
>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 |
### 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
---------------------------------------------------------------
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### 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
---------------------------------------------------------------
|
| 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 | Motif detection |
| 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 |
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.