Provider:
Center for Biological Sequence Analysis (CBS)
Location:
Denmark
Submitter / Source:
Franck Tanoh (about 1 year 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)
Documentation URL(s): Franck Tanoh (about 1 year ago)http://www.cbs.dtu.dk/ws/ws.php?entry=EasyGene
rapacki (3 months ago)http://www.cbs.dtu.dk/services/EasyGene/
Login to add a documentation URL Description(s): from provider’s description doc (about 1 year 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
BPS01Burkholderia pseudomallei K96243
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
Franck Tanoh (about 1 year ago)Produces a list of predicted genes given a sequence of prokaryotic DNA.
Interface: http://www.cbs.dtu.dk/services/EasyGene/
kwolstencroft (11 months ago)A gene prediction service for prokaryotic DNA
rapacki (3 months 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.
Alongside this Web Service EasyGene method is also implemented as an interactive server at: http://www.cbs.dtu.dk/services/EasyGene/
Login to add a description License(s): None Login to add license info Cost: No info yet Login to add cost info Usage Conditions: No info yet Login to add usage conditions info Contact Info: None Login to add contact info Publications: for this service. This can be a URI to the publication and/or a DOI. None Login to add publication info Citations: None Login to add a citation