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EasyGene 1.2a.ws0

Prediction of genes in prokaryotes

NOTE: a newer version of this service (EasyGene 1.2a.ws1) is available.

WSDL EasyGene/EasyGene_1_2a_ws0.wsdl
Schema definitions ../common/ws_common_1_0b.xsd
ws_easygene_1_2a_ws0.xsd

We recommend that the first time users should load the WSDL file above to SoapUI and investigate the Web Service operations in that environment. SoapUI is a desktop application for inspecting, invoking, developing and functional/load/compliance testing of Web Services over HTTP. It can be downloaded free of charge from http://www.soapui.org/.

Other versions and implementations

Ver.Last updated
1.2a.ws1  2012-04-19(most recent)
1.2a.ws0  2007-03-27(this version)
1.2  2008-02-13

Examples of client side scripts using the service

FilenameTypeCompatibilityAuthorDescription
easygene_java (6.5 KB) Java 1.2a ws1 Karunakar Bayyapu
Client script in Java (apache) running the EasyGene Web Service
easygene.pl (2.1 KB) Perl 1.2 Peter Fischer Hallin
Read any number of fasta entries of prokaryotic DNA from STDIN and predict open reading frames
getseq.pl (973 B) Perl Genome Atlas 3.0.ws2 Peter Fischer Hallin
Download genome sequence of a genbank accession no.
easygene_soap_analysis (8.3 KB) 1.2a ws1 Karunakar Bayyapu
Detailed analysis of SOAP and WSDL versions with supported clients
easygene_perl2 (5.4 KB) Perl 1.2a ws1 Karunakar Bayyapu
Client script in Perl (XML::Compile) running the EasyGene Web Service
easygene_perl1 (5.6 KB) Perl 1.2a ws1 Karunakar Bayyapu
Client script in Perl (SOAP::Lite) running the EasyGene Web Service
easygene_php (4.6 KB) PHP 1.2a ws1 Karunakar Bayyapu
Client script in PHP running the EasyGene Web Service
easygene_python (4.9 KB) Python 1.2a ws1 Karunakar Bayyapu
Client script in Python (suds) running the EasyGene Web Service
easygene_csharp (5.5 KB) C# 1.2a ws1 Karunakar Bayyapu
Client script in C# (mono) running the EasyGene Web Service
xml-compile.pl (3.2 KB) Perl NA Peter Fischer Hallin
Helper scripts used to initiate XML::Compile's proxys (WSDL+XSD)

Usage

# download the required scripts
wget http://www.cbs.dtu.dk/ws/EasyGene/examples/xml-compile.pl
wget http://www.cbs.dtu.dk/ws/EasyGene/examples/getseq.pl
wget http://www.cbs.dtu.dk/ws/EasyGene/examples/easygene.pl
# run gene prediction, using model CJ02 (Campylobacter jejuni)
perl getseq.pl CP000055 | perl easygene.pl 2.0 CJ02

Documentation

 
  The EasyGene 1.0 server produces a list of predicted genes given a sequence of prokaryotic 
  DNA. Each prediction is attributed with a significance score (R-value) indicating how likely 
  it is to be just a non-coding open reading frame rather than a real gene. The user needs 
  only to specify the organism hosting the query sequence. Two more parameters (start codon 
  leniency and R-value cutoff) have default values which may be altered if needed.

    http://www.cbs.dtu.dk/services/EasyGene/

  This service is fully asynchronous;  the usage is split into the following
  three operations, which is usually executed in this order.
  
  Procedures and messages used are either common and shared among all the CBS
  Web Services, or distinct to each individual Web Service. Marked [distinct] and
  [common] respectively.

  1. runService [distinct/common]
    Submit the input parapeter(s) and sequence data and returns a job identifier

    Input: [distinct]
          * 'Rvalue' - R-value cutoff (default 2)
          * 'model' - Organism abbreviation for model:
                AP02  Aeropyrum pernix 
                ATW03  Agrobacterium tumefaciens str. C58
                AA02  Aquifex aeolicus 
                AF02  Archaeoglobus fulgidus DSM 4304 
                BAA03  Bacillus anthracis str. Ames 
                BCE03  Bacillus cereus ATCC 10987 
                BH03  Bacillus halodurans 
                BPS01  Burkholderia pseudomallei K96243
                BS03  Bacillus subtilis 
                BT02  Bacteroides thetaiotaomicron VPI-5482 
                BBA01  Bdellovibrio bacteriovorus 
                BL03  Bifidobacterium longum NCC2705 
                BBR02  Bordetella bronchiseptica 
                BPA02  Bordetella parapertussis 
                BPE02  Bordetella pertussis 
                BJ02  Bradyrhizobium japonicum 
                BM02  Brucella melitensis
                BSU03  Brucella suis 1330
                BAS02  Buchnera aphidicola
                CJ02  Campylobacter jejuni 
                CF02  Candidatus Blochmannia floridanus 
                CC02  Caulobacter crescentus CB15 
                CM02  Chlamydia muridarum  
                CPN03  Chlamydia pneumoniae AR39 
                CT02  Chlamydia trachomatis 
                CCA02  Chlamydophila caviae GPIC    
                CTE02  Chlorobium tepidum TLS 
                CV02  Chromobacterium violaceum ATCC 12472  
                CA02  Clostridium acetobutylicum ATCC824  
                CP02  Clostridium perfringens 
                CTEE02  Clostridium tetani E88 
                CDI01  Corynebacterium diphtheriae 
                CEF01  Corynebacterium efficiens YS-314 
                CG03  Corynebacterium glutamicum ATCC 13032 
                CB02  Coxiella burnetii RSA 493 
                DR02  Deinococcus radiodurans
                EF02  Enterococcus faecalis V583 
                ECC02  Escherichia coli CFT073 
                EC03  Escherichia coli K12 
                ECE03  Escherichia coli O157:H7 EDL933 
                ECO02  Escherichia coli O157:H7  
                FN02  Fusobacterium nucleatum subsp. nucleatum ATCC 2558... 
                GS01  Geobacter sulfurreducens PCA 
                GV01  Gloeobacter violaceus 
                HD02  Haemophilus ducreyi 35000HP 
                HI02  Haemophilus influenzae Rd 
                HM01  Haloarcula marismortui ATCC 43049
                HS02  Halobacterium sp. NRC-1 
                HW01  Haloquadratum walsbyi DSM 16790  
                HP02  Helicobacter pylori 26695 
                HPJ02  Helicobacter pylori str. J99 
                LJ01  Lactobacillus johnsonii NCC 533 
                LP02  Lactobacillus plantarum WCFS1 
                LL02  Lactococcus lactis subsp. lactis 
                LIN02  Leptospira interrogans serovar lai str. 56601 
                LI02  Listeria innocua Clip11262 
                LM02  Listeria monocytogenes EGD 
                MLO03  Mesorhizobium loti 
                MET02  Methanobacterium thermoautotrophicum str. Delta H 
                MBU01  Methanococcoides burtonii DSM 6242 
                MJ02  Methanococcus jannaschii 
                MM01  Methanococcus maripaludis S2 
                MK02  Methanopyrus kandleri AV19 
                MTE01  Methanosaeta thermophila PT 
                MA02  Methanosarcina acetivorans str. C2A 
                MBA01  Methanosarcina barkeri str. fusaro
                MM02  Methanosarcina mazei Goe1 
                MST01  Methanosphaera stadtmanae DSM 3091 
                MHU01  Methanospirillum hungatei JF-1 
                MAP01  Mycobacterium avium subsp. paratuberculosis str. k... 
                MB02  Mycobacterium bovis subsp. bovis AF2122/97 
                MT03  Mycobacterium tuberculosis CDC1551 
                MTH03  Mycobacterium tuberculosis H23Rv 
                NEQ01  Nanoarchaeum equitans Kin4-M 
                NP01  Natronomonas pharaonis DSM 2160 
                NMA02  Neisseria meningitidis serogroup A Z2491 
                NM02  Neisseria meningitidis serogroup B MC58 
                NE02  Nitrosomonas europaea 
                NO02  Nostoc sp. PCC 7120 
                OI02  Oceanobacillus iheyensis HTE831 
                OYP01  Onion yellows phytoplasma 
                PM02  Pasteurella multocida 
                PL01  Photorhabdus luminescens subsp. laumondii TTO1 
                PT01  Picrophilus torridus DSM 9790 
                PI02  Pirellula sp 
                PG02  Porphyromonas gingivalis W83 
                PMMI02  Prochlorococcus marinus str. MIT 9313 
                PMA02  Prochlorococcus marinus subsp marinus CCMP1375 
                PMM02  Prochlorococcus marinus subsp. pastoris str. CCMP1... 
                PA02  Pseudomonas aeruginosa PA01 
                PS02  Pseudomonas syringae pv. tomato str. DC3000 
                PAE02  Pyrobaculum aerophilum 
                PRI01  Pyrobaculum islandicum DSM 4184 
                PAB02  Pyrococcus abyssi 
                PF02  Pyrococcus furiosus DSM 3638 
                PH02  Pyrococcus horikoshii 
                RS02  Ralstonia solanacearum
                RPA01  Rhodopseudomonas palustris CGA009 
                RC02  Rickettsia conorii Malish 7 
                RP02  Rickettsia prowazekii Madrid E 
                SE02  Salmonella enterica subsp. enterica serovar Typhi ... 
                STT02  Salmonella enterica subsp. enterica serovar Typhi ... 
                STY02  Salmonella typhimurium LT2 
                SO02  Shewanella oneidensis MR-1 
                SM02  Sinorhizobium meliloti 1021 
                SAM03  Staphylococcus aureus MU50  
                SA02  Staphylococcus aureus subsp aureus N315 
                SEA02  Staphylococcus epidermidis ATCC 12228 
                SAG02  Streptococcus agalactiae 2603V/R 
                SAN02  Streptococcus agalactiae NEM316 
                SMU02  Streptococcus mutans UA159 
                SP02  Streptococcus pneumoniae
                SPY02  Streptococcus pyogenes 
                SAV03  Streptomyces avermitilis MA-4680 
                SC02  Streptomyces coelicolor A3(2) 
                UC01  Sulfolobus acidocaldarius DSM 639 
                SS02  Sulfolobus solfataricus 
                ST02  Sulfolobus tokodaii 
                SSW02  Synechococcus sp. WH 8102 
                SPC02  Synechocystis sp. PCC 6803 
                TT02  Thermoanaerobacter tengcongensis strain MB4T 
                TK01  Thermococcus kodakarensis KOD1  
                THP01  Thermofilum pendens Hrk 5 
                TA02  Thermoplasma acidophilum 
                TV02  Thermoplasma volcanium 
                TE02  Thermosynechococcus elongatus BP-1 
                TM02  Thermotoga maritima 
                TD01  Treponema denticola ATCC 35405 
                TP02  Treponema pallidum 
                TW02  Tropheryma whipplei Twist 
                VC02  Vibrio cholerae 
                VP02  Vibrio parahaemolyticus RIMD 2210633
                VV02  Vibrio vulnificus
                WB02  Wigglesworthia glossinidia endosymbiont of Glossin... 
                WDM01  Wolbachia endosymbiont of Drosophila melanogaster 
                XA02  Xanthomonas axonopodis pv. citri str. 306 
                XC02  Xanthomonas campestris pv. campestris str. ATCC 33... 
                XF02  Xylella fastidiosa
                YP02  Yersinia pestis
          * 'sequencedata' [STANDARD SEQUENCE DATA TYPE]
            * 'sequence' - An array of sequence objects, containing the following elements:
              * 'id' - The identifier of the sequence
              * 'comment' - optiona
              * 'seq' - The sequence specified as one continous string
    Output: [STANDARD ANNOTATION TYPE]
          * 'jobid' - The 32 byte identification string of the job
          * 'datetime' - The last timepoint at which the status of the job has changed
          * 'status' - Possible values are QUEUED, ACTIVE, FINISHED, WAITING, REJECTED, 
            UNKNOWN JOBID or QUEUE DOWN
    
  2. pollQueue [common]
  Once obtained from 'runService', a job identification can be used to poll the
  status to see if the result is ready for download.

    Input:   [common]
          * 'jobid' - The 32 byte identification string of the job
    Output:  [common]
          * 'jobid' - The 32 byte identification string of the job
          * 'datetime' - The last timepoint at which the status of the job has changed
          * 'status' - Possible values are QUEUED, ACTIVE, FINISHED, WAITING, REJECTED, 
            UNKNOWN JOBID or QUEUE DOWN

  3. fetchResult  [distinct/common]
  Once the status is 'FINISHED' the results generated by the Web Service can be retrieved by
  specifying the jobid;
  
    Input:   [common]
          * 'jobid' - The 32 byte identification string of the job
    Output:  [distinct]
          *  'predictionTitle' - Short description of the generated output
          *  'predictor' - Name and version of the program which generated the output
          *  'reference' - Publication / reference of the method
          *  'predictionDate' - Date at the time the when the prediction finished
          *  'entries' - A collection of gene predictions containing the following information:
           *    'sequence' - The sequence name
           *    'feature' - Feature type (CDS)
           *    'begin' - Start position of the gene (integer)
           *    'end' - stop position of the gene (integer)
           *    'Rvalue' - R-value for the prediction
           *    'strand' - strand of the gene (+/-)
           *    'start' - Start codon
           *    'logOdds' - The log odds score