Web Service EasyGene - Prediction of genes in prokaryotes SOAP Dk

Cog_error Archived / Deprecated

This service has been archived because it may not be active anymore (or is close to being non active). Please do not use it as it may not be accessible.

Specified Name (from WSDL): WSEasyGene_1_2a_ws0 |
UNCHECKED
Annotations: 27 Total number of annotations from the provider's definition / description document. 1 Total number of annotations submitted by members of BioCatalogue. 19 Total number of annotations sourced from other registries. 7

Overview

Provider:
Center for Biological Sequence Analysis (CBS)

Location:
Denmark Dk

Submitter/Source:
Franck TanohGb (over 11 years ago)

Base URL:
http://ws.cbs.dtu.dk/cgi-bin/soap/ws/quasi-1.2.cgi

WSDL Location:
http://www.cbs.dtu.dk/ws/EasyGene/EasyGene_1_2a_ws0.wsdl (download last cached WSDL file)

Description(s):
from provider's description doc (over 11 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:
							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
by Franck Tanoh (over 11 years ago)

Produces a list of predicted genes given a sequence of prokaryotic DNA. Interface: http://www.cbs.dtu.dk/services/EasyGene/

by kwolstencroft (over 11 years ago)

A gene prediction service for prokaryotic DNA

by rapacki (over 10 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 g

ELIXIR Description(s): Info
No info yet
License(s): Info
No info yet
Cost: Info
No info yet
Usage conditions: Info
No info yet
Contact info: Info
No info yet
How to cite this service: Info
No info yet
Publications about this service: Info
No info yet
Citations of this service: Info
No info yet

Info Members Responsible for this Service (1)

Info Favourited By (1)

Info Similar Services (99)