Provider:
Center for Biological Sequence Analysis (CBS)
Location:
Denmark
Submitter/Source:
SeekDa (over 6 years ago)
Base URL:
http://ws.cbs.dtu.dk/cgi-bin/soap/ws/quasi.cgi
WSDL Location:
http://www.cbs.dtu.dk/ws/EasyGene/EasyGene_1_2.wsdl(download last cached WSDL file)
Documentation URL(s): None Login to add a documentation URL Description(s): from provider’s description doc (over 6 years ago) 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: AP02Aeropyrum pernix ATW03Agrobacterium tumefaciens str. C58 AA02Aquifex aeolicus AF02Archaeoglobus fulgidus DSM 4304 BAA03Bacillus anthracis str. Ames BCE03Bacillus cereus ATCC 10987 BH03Bacillus halodurans BS03Bacillus subtilis BT02Bacteroides thetaiotaomicron VPI-5482 BBA01Bdellovibrio bacteriovorus BL03Bifidobacterium longum NCC2705 BBR02Bordetella bronchiseptica BPA02Bordetella parapertussis BPE02Bordetella pertussis BJ02Bradyrhizobium japonicum BM02Brucella melitensis BSU03Brucella suis 1330 BAS02Buchnera aphidicola CJ02Campylobacter jejuni CF02Candidatus Blochmannia floridanus CC02Caulobacter crescentus CB15 CM02Chlamydia muridarum CPN03Chlamydia pneumoniae AR39 CT02Chlamydia trachomatis CCA02Chlamydophila caviae GPIC CTE02Chlorobium tepidum TLS CV02Chromobacterium violaceum ATCC 12472 CA02Clostridium acetobutylicum ATCC824 CP02Clostridium perfringens CTEE02Clostridium tetani E88 CDI01Corynebacterium diphtheriae CEF01Corynebacterium efficiens YS-314 CG03Corynebacterium glutamicum ATCC 13032 CB02Coxiella burnetii RSA 493 DR02Deinococcus radiodurans EF02Enterococcus faecalis V583 ECC02Escherichia coli CFT073 EC03Escherichia coli K12 ECE03Escherichia coli O157:H7 EDL933 ECO02Escherichia coli O157:H7 FN02Fusobacterium nucleatum subsp. nucleatum ATCC 2558… GS01Geobacter sulfurreducens PCA GV01Gloeobacter violaceus HD02Haemophilus ducreyi 35000HP HI02Haemophilus influenzae Rd HM01Haloarcula marismortui ATCC 43049 HS02Halobacterium sp. NRC-1 HW01Haloquadratum walsbyi DSM 16790 HP02Helicobacter pylori 26695 HPJ02Helicobacter pylori str. J99 LJ01Lactobacillus johnsonii NCC 533 LP02Lactobacillus plantarum WCFS1 LL02Lactococcus lactis subsp. lactis LIN02Leptospira interrogans serovar lai str. 56601 LI02Listeria innocua Clip11262 LM02Listeria monocytogenes EGD MLO03Mesorhizobium loti MET02Methanobacterium thermoautotrophicum str. Delta H MBU01Methanococcoides burtonii DSM 6242 MJ02Methanococcus jannaschii MM01Methanococcus maripaludis S2 MK02Methanopyrus kandleri AV19 MTE01Methanosaeta thermophila PT MA02Methanosarcina acetivorans str. C2A MBA01Methanosarcina barkeri str. fusaro MM02Methanosarcina mazei Goe1 MST01Methanosphaera stadtmanae DSM 3091 MHU01Methanospirillum hungatei JF-1 MAP01Mycobacterium avium subsp. paratuberculosis str. k… MB02Mycobacterium bovis subsp. bovis AF2122/97 MT03Mycobacterium tuberculosis CDC1551 MTH03Mycobacterium tuberculosis H23Rv NEQ01Nanoarchaeum equitans Kin4-M NP01Natronomonas pharaonis DSM 2160 NMA02Neisseria meningitidis serogroup A Z2491 NM02Neisseria meningitidis serogroup B MC58 NE02Nitrosomonas europaea NO02Nostoc sp. PCC 7120 OI02Oceanobacillus iheyensis HTE831 OYP01Onion yellows phytoplasma PM02Pasteurella multocida PL01Photorhabdus luminescens subsp. laumondii TTO1 PT01Picrophilus torridus DSM 9790 PI02Pirellula sp PG02Porphyromonas gingivalis W83 PMMI02Prochlorococcus marinus str. MIT 9313 PMA02Prochlorococcus marinus subsp marinus CCMP1375 PMM02Prochlorococcus marinus subsp. pastoris str. CCMP1… PA02Pseudomonas aeruginosa PA01 PS02Pseudomonas syringae pv. tomato str. DC3000 PAE02Pyrobaculum aerophilum PRI01Pyrobaculum islandicum DSM 4184 PAB02Pyrococcus abyssi PF02Pyrococcus furiosus DSM 3638 PH02Pyrococcus horikoshii RS02Ralstonia solanacearum RPA01Rhodopseudomonas palustris CGA009 RC02Rickettsia conorii Malish 7 RP02Rickettsia prowazekii Madrid E SE02Salmonella enterica subsp. enterica serovar Typhi … STT02Salmonella enterica subsp. enterica serovar Typhi … STY02Salmonella typhimurium LT2 SO02Shewanella oneidensis MR-1 SM02Sinorhizobium meliloti 1021 SAM03Staphylococcus aureus MU50 SA02Staphylococcus aureus subsp aureus N315 SEA02Staphylococcus epidermidis ATCC 12228 SAG02Streptococcus agalactiae 2603V/R SAN02Streptococcus agalactiae NEM316 SMU02Streptococcus mutans UA159 SP02Streptococcus pneumoniae SPY02Streptococcus pyogenes SAV03Streptomyces avermitilis MA-4680 SC02Streptomyces coelicolor A3(2) UC01Sulfolobus acidocaldarius DSM 639 SS02Sulfolobus solfataricus ST02Sulfolobus tokodaii SSW02Synechococcus sp. WH 8102 SPC02Synechocystis sp. PCC 6803 TT02Thermoanaerobacter tengcongensis strain MB4T TK01Thermococcus kodakarensis KOD1 THP01Thermofilum pendens Hrk 5 TA02Thermoplasma acidophilum TV02Thermoplasma volcanium TE02Thermosynechococcus elongatus BP-1 TM02Thermotoga maritima TD01Treponema denticola ATCC 35405 TP02Treponema pallidum TW02Tropheryma whipplei Twist VC02Vibrio cholerae VP02Vibrio parahaemolyticus RIMD 2210633 VV02Vibrio vulnificus WB02Wigglesworthia glossinidia endosymbiont of Glossin… WDM01Wolbachia endosymbiont of Drosophila melanogaster XA02Xanthomonas axonopodis pv. citri str. 306 XC02Xanthomonas campestris pv. campestris str. ATCC 33… XF02Xylella fastidiosa YP02Yersinia 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
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