EasyGene – Prediction of genes in prokaryotes

By | September 22, 2011

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

Name
EasyGene – Prediction of genes in prokaryotes
Documentation
http://www.cbs.dtu.dk/services/EasyGene/
http://www.cbs.dtu.dk/ws/ws.php?entry=EasyGene
Protocol
SOAP
WSDL
Endpoint
http://ws.cbs.dtu.dk/cgi-bin/soap/ws/quasi-1.2.cgi
Topic
Gene Prediction
Type
Analysis
Tags
, , , , , , , , ,
Description

The EasyGene 1.0 server produces a list of predicted genes given a sequence of prokaryotic DNA. Each prediction is attributed [...]

Further information

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

Original source
BioCatalogue

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