Functional Gene Pipeline and Repository

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If you use RDP's FunGene, please cite our most recent article.


Begin with these gene links:
Version 9.5 -- GenBank 223 (as of 2/16/2018)
Process your own Functional Gene data using our new FunGene Pipeline

Antibiotic resistances
genecontributor
ACTSyed Hashsham
BELSyed Hashsham
beta_IS6Robert Stedtfeld
beta_tnpARobert Stedtfeld
beta_tnpA2Robert Stedtfeld
bet_blaSHVRobert Stedtfeld
bet_tnpARobert Stedtfeld
CARBSyed Hashsham
cefa_qacEdeltaRobert Stedtfeld
chl_cmlARobert Stedtfeld
CMYSyed Hashsham
cprATamara Tsoi Cole
cprBTamara Tsoi Cole
CTX-MSyed Hashsham
dfra1Syed Hashsham
dfra12Syed Hashsham
dfrA7Xun Qian
FOXSyed Hashsham
gapATim Johnson
GESSyed Hashsham
IMISyed Hashsham
IMPSyed Hashsham
IncW_trwATim Johnson
IncW_trwBTim Johnson
INDSyed Hashsham
intICarlos Rodriguez-Minguela
intI1Xun Qian
intI1_sub1Tim Johnson
intI2Xun Qian
intI2Tim Johnson
intI3Tim Johnson
KPCSyed Hashsham
mdh_sub1Tim Johnson
mdh_sub2Tim Johnson
MIRSyed Hashsham
MOXSyed Hashsham
NDMSyed Hashsham
OXASyed Hashsham
pec_aad2Robert Stedtfeld
PERSyed Hashsham
qacEdelta1Xun Qian
repATim Johnson
SHVSyed Hashsham
SMESyed Hashsham
spec_aad1Robert Stedtfeld
strARobert Stedtfeld
strBRobert Stedtfeld
strept_aadRobert Stedtfeld
TEMSyed Hashsham
tet1Robert Stedtfeld
tet2Robert Stedtfeld
tet3Robert Stedtfeld
tet31Syed Hashsham
tet4Robert Stedtfeld
tetMCarlos Rodriguez-Minguela
tetQCarlos Rodriguez-Minguela
tet_sul2Robert Stedtfeld
tetWCarlos Rodriguez-Minguela
vanc_unnameRobert Stedtfeld
VEBSyed Hashsham
VIMSyed Hashsham
Plant Pathogenicity
genecontributor
avrEJames Kremer
txtARDP
txtBRDP
Biogeochemical cycles
genecontributor
ALPAlan Richardson
alp_newJiangbin Xu
amoA_AOAFeifei Liu
amoA_AOBRDP
amoA_AOB_likeBingbing Li
amoA_comammoxYang Ouyang
anfDYang Ouyang
BPPAlan Richardson
bukRDP
butRDP
cbh1Cheryl Kuske
chbFan Yang
cooSFan Yang
cydARachel Morris
dsrAAlexander Loy/Michael Wagner
dsrBAlexander Loy/Michael Wagner
exc1Fan Yang
fixNRachel Morris
glxQichao Tu
HAPAlan Richardson
hydAFan Yang
lcc_ascomycetesChris Wright
lcc_basidiomycetesChris Wright
ligERyan Penton
lipQichao Tu
mcrABlaz Stres
mmoXQichao Tu
mnpQichao Tu
nag3Fan Yang
napALaurent Philippot
narGLaurent Philippot
nifDRDP
nifHRDP
nirARDP
nirBRDP
nirKTracy Teal
nirSVeronica Gruntzig
norBGesche Braker
nosZBlaz Stres
nosZ_atypical_1Robert Sanford
nosZ_atypical_2Robert Sanford
nrfAJoel Klappenbach
nrfA_WelshAllana Welsh
nxrA_nitrobacterYang Ouyang
nxrBRDP
nxrB_nitrobacterYang Ouyang
nxrB_nitrospiraYang Ouyang
p450norSteven Higgins
PAPAlan Richardson
phnXZarraz Lee
phoDElizabeth Bent
pmoATracy K. Teal
pmoA_1a_1bBingbing Li
pmoA_2a_2bBingbing Li
pmoA_Crenothrix_likeBingbing Li
pmoA_M84_P105_likeBingbing Li
pmoA_RA21_likeBingbing Li
pmoA_TUSC_likeBingbing Li
pmoA_type1aBingbing Li
pmoA_type1bBingbing Li
pmoA_type2aBingbing Li
pmoA_type2bBingbing Li
ppoQichao Tu
PTPAlan Richardson
scd2RDP
soxBGupta Vadakattu
vnfDYang Ouyang
vnfD_anfDYang Ouyang
vp1Chris Wright
xylAQichao Tu
Phylogenetic markers
genecontributor
EF-TuJames Kremer
fusAScott Santos/Howard Ochman
gyrBZarraz May-Ping Lee
ileSScott Santos/Howard Ochman
lepAScott Santos/Howard Ochman
leuSScott Santos/Howard Ochman
pyrGScott Santos/Howard Ochman
recAScott Santos/Howard Ochman
recGScott Santos/Howard Ochman
rplBScott Santos/Howard Ochman
rplB_arcRuonan Wu
rpoBScott Santos/Howard Ochman
rpsCJiarong Guo
Antibiotic resistances II
genecontributor
aac2iSyed Hashsham
aac2iaSyed Hashsham
aac2ibSyed Hashsham
aac2icSyed Hashsham
aac2idSyed Hashsham
aac3iaSyed Hashsham
aac3iiaSyed Hashsham
aac3iibSyed Hashsham
aac3iiiSyed Hashsham
aac3ivSyed Hashsham
aac3ixSyed Hashsham
aac3viiSyed Hashsham
aac3viiiSyed Hashsham
aac3xSyed Hashsham
aac6iSyed Hashsham
aac6iaSyed Hashsham
aac6icSyed Hashsham
aac6ieSyed Hashsham
aac6ifSyed Hashsham
aac6igSyed Hashsham
aac6iiaSyed Hashsham
aac6iibSyed Hashsham
aad9Syed Hashsham
aad9ibSyed Hashsham
acet_catBRobert Stedtfeld
acety_satRobert Stedtfeld
acety_vatRobert Stedtfeld
acrbSyed Hashsham
adeaSyed Hashsham
adebSyed Hashsham
adecSyed Hashsham
amik_aacRobert Stedtfeld
amin_aphRobert Stedtfeld
amino_aadKRobert Stedtfeld
amraSyed Hashsham
amrbSyed Hashsham
ant2ibSyed Hashsham
ant4iiaSyed Hashsham
ant6iaSyed Hashsham
aph33iaSyed Hashsham
aph33ibSyed Hashsham
aph3iaSyed Hashsham
aph3ibSyed Hashsham
aph3icSyed Hashsham
aph3ivaSyed Hashsham
aph3vaSyed Hashsham
aph3vbSyed Hashsham
aph3viaSyed Hashsham
aph3viiaSyed Hashsham
aph4ibSyed Hashsham
aph6iaSyed Hashsham
aph6ibSyed Hashsham
aph6icSyed Hashsham
apsATim Johnson
arnaSyed Hashsham
ATP_vgaRobert Stedtfeld
bac_bacARobert Stedtfeld
bac_bacA2Robert Stedtfeld
bcraSyed Hashsham
bcrcSyed Hashsham
beta_blaCMYRobert Stedtfeld
beta_blaIMPRobert Stedtfeld
beta_blaVIMRobert Stedtfeld
beta_ccraRobert Stedtfeld
beta_cfiARobert Stedtfeld
beta_imiRRobert Stedtfeld
beta_intI1Robert Stedtfeld
beta_nmc-RRobert Stedtfeld
bet_ompKRobert Stedtfeld
bl1_accSyed Hashsham
bl1_asbaSyed Hashsham
bl1_cepsSyed Hashsham
bl1_ecSyed Hashsham
bl1_foxSyed Hashsham
bl1_moxSyed Hashsham
bl1_ochSyed Hashsham
bl1_paoSyed Hashsham
bl1_pseSyed Hashsham
bl2a_1Syed Hashsham
bl2a_exoSyed Hashsham
bl2a_iiiSyed Hashsham
bl2a_iii2Syed Hashsham
bl2a_kccSyed Hashsham
bl2a_npsSyed Hashsham
bl2a_okpSyed Hashsham
bl2be_oxy1Syed Hashsham
bl2b_robSyed Hashsham
bl2b_temSyed Hashsham
bl2b_tem2Syed Hashsham
bl2b_tleSyed Hashsham
bl2b_ulaSyed Hashsham
bl2c_broSyed Hashsham
bl2c_pse1Syed Hashsham
bl2c_pse3Syed Hashsham
bl2d_lcr1Syed Hashsham
bl2d_moxaSyed Hashsham
bl2d_oxa10Syed Hashsham
bl2d_oxa5Syed Hashsham
bl2d_oxa9Syed Hashsham
bl2d_r39Syed Hashsham
bl2e_cblaSyed Hashsham
bl2e_fpmSyed Hashsham
bl2e_y56Syed Hashsham
bl2f_nmcaSyed Hashsham
bl2f_sme1Syed Hashsham
bl2_kpcSyed Hashsham
bl2_lenSyed Hashsham
bl2_vebSyed Hashsham
bl3_ccraSyed Hashsham
bl3_citSyed Hashsham
bl3_cphaSyed Hashsham
bl3_gimSyed Hashsham
bl3_lSyed Hashsham
bl3_shwSyed Hashsham
bl3_simSyed Hashsham
bltSyed Hashsham
bmrSyed Hashsham
caraSyed Hashsham
cata10Syed Hashsham
cata11Syed Hashsham
cata13Syed Hashsham
cata14Syed Hashsham
cata15Syed Hashsham
cata16Syed Hashsham
cata2Syed Hashsham
cata3Syed Hashsham
cata4Syed Hashsham
cata5Syed Hashsham
cata6Syed Hashsham
catb1Syed Hashsham
catb2Syed Hashsham
catb3Syed Hashsham
catb4Syed Hashsham
catb5Syed Hashsham
cefa_ampcRobert Stedtfeld
cefa_oxaRobert Stedtfeld
cefe_QacdeltaRobert Stedtfeld
ceoaSyed Hashsham
ceobSyed Hashsham
cfr3Robert Stedtfeld
chlo_CMRRobert Stedtfeld
chlor_araJRobert Stedtfeld
chlo_rarDRobert Stedtfeld
cipr_grlARobert Stedtfeld
cipr_grlA2Robert Stedtfeld
cipr_grlA3Robert Stedtfeld
cipr_grlA4Robert Stedtfeld
cipr_grlA5Robert Stedtfeld
cipr_gyrA1Robert Stedtfeld
clind_cfrRobert Stedtfeld
clind_cfr2Robert Stedtfeld
clind_rrnaRobert Stedtfeld
cml_e2Syed Hashsham
cml_e3Syed Hashsham
cml_e5Syed Hashsham
cml_e6Syed Hashsham
cml_e7Syed Hashsham
cml_e8Syed Hashsham
dfra10Syed Hashsham
dfra13Syed Hashsham
dfra14Syed Hashsham
dfra15Syed Hashsham
dfra16Syed Hashsham
dfra17Syed Hashsham
dfra19Syed Hashsham
dfra20Syed Hashsham
dfra21Syed Hashsham
dfra22Syed Hashsham
dfra23Syed Hashsham
dfra24Syed Hashsham
dfra25Syed Hashsham
dfra26Syed Hashsham
dfra5Syed Hashsham
dfra7Syed Hashsham
dfrb1Syed Hashsham
dfrb2Syed Hashsham
dfrb3Syed Hashsham
dfrb6Syed Hashsham
doxy_tetMRobert Stedtfeld
efflux_metRobert Stedtfeld
emrdSyed Hashsham
emreSyed Hashsham
ereaSyed Hashsham
erebSyed Hashsham
ermdSyed Hashsham
ermeSyed Hashsham
ermgSyed Hashsham
ermhSyed Hashsham
ermnSyed Hashsham
ermoSyed Hashsham
ermqSyed Hashsham
ermrSyed Hashsham
ermsSyed Hashsham
ermuSyed Hashsham
ermvSyed Hashsham
ermwSyed Hashsham
eryt_ermRobert Stedtfeld
eryt_erm1Robert Stedtfeld
eryt_erm2Robert Stedtfeld
eryt_erm3Robert Stedtfeld
eryt_msrRobert Stedtfeld
fosaSyed Hashsham
fosbSyed Hashsham
foscSyed Hashsham
fosxSyed Hashsham
fosy_fosBRobert Stedtfeld
fushSyed Hashsham
gent_aacRobert Stedtfeld
gent_aac2Robert Stedtfeld
gent_aac3Robert Stedtfeld
gent_aac4Robert Stedtfeld
hydro_vgbRobert Stedtfeld
intI1_sub2Tim Johnson
ison_katGRobert Stedtfeld
kana_aahDRobert Stedtfeld
kana_aph2Robert Stedtfeld
ksgaSyed Hashsham
lmrbSyed Hashsham
lsaSyed Hashsham
macaSyed Hashsham
macbSyed Hashsham
mdteSyed Hashsham
mdtfSyed Hashsham
mdtgSyed Hashsham
mdthSyed Hashsham
mdtkSyed Hashsham
mdtlSyed Hashsham
mdtmSyed Hashsham
mdtnSyed Hashsham
mdtoSyed Hashsham
mdtpSyed Hashsham
mexaSyed Hashsham
mexcSyed Hashsham
mexdSyed Hashsham
mexhSyed Hashsham
mexiSyed Hashsham
mexwSyed Hashsham
mexxSyed Hashsham
mexySyed Hashsham
mfpaSyed Hashsham
mphaSyed Hashsham
neom_aph2Robert Stedtfeld
nitro_nimRobert Stedtfeld
normSyed Hashsham
olebSyed Hashsham
opcmSyed Hashsham
opraSyed Hashsham
oprdSyed Hashsham
oprjSyed Hashsham
oprmSyed Hashsham
oprnSyed Hashsham
otraSyed Hashsham
otrbSyed Hashsham
pbp1aSyed Hashsham
pbp1bSyed Hashsham
pbp2Syed Hashsham
pbp2bSyed Hashsham
pbp2xSyed Hashsham
pen_mecARobert Stedtfeld
pmraSyed Hashsham
pyaz_pncARobert Stedtfeld
qnraSyed Hashsham
qnrbSyed Hashsham
qnrsSyed Hashsham
refa_rpoBRobert Stedtfeld
refa_rpoB1Robert Stedtfeld
rifa_rpbRobert Stedtfeld
rifa_rpoBRobert Stedtfeld
rifa_rpoB2Robert Stedtfeld
rifa_unnamedRobert Stedtfeld
rosaSyed Hashsham
rosbSyed Hashsham
smeaSyed Hashsham
smebSyed Hashsham
smecSyed Hashsham
smedSyed Hashsham
smeeSyed Hashsham
smefSyed Hashsham
spec_aadRobert Stedtfeld
spec_aad3Robert Stedtfeld
spec_aad4Robert Stedtfeld
spec_aphRobert Stedtfeld
spec_spcNRobert Stedtfeld
srmbSyed Hashsham
staSyed Hashsham
stre_aphERobert Stedtfeld
sul1Syed Hashsham
sul3Syed Hashsham
sulp_sulRobert Stedtfeld
tcmaSyed Hashsham
tcr3Syed Hashsham
tetSyed Hashsham
tetRobert Stedtfeld
tet33Syed Hashsham
tet39Syed Hashsham
tet40Syed Hashsham
tetcSyed Hashsham
tetCRobert Stedtfeld
teteSyed Hashsham
tet_otrBRobert Stedtfeld
tetpbSyed Hashsham
tetSRobert Stedtfeld
tettSyed Hashsham
tetySyed Hashsham
tet_yyaRobert Stedtfeld
tetzSyed Hashsham
tlrcSyed Hashsham
tmrbSyed Hashsham
tobr_aacA4Robert Stedtfeld
tolcSyed Hashsham
tran_lnuBRobert Stedtfeld
trim_dfrRobert Stedtfeld
trova_grlA6Robert Stedtfeld
trova_grlA7Robert Stedtfeld
trovA_grlA8Robert Stedtfeld
tsnrSyed Hashsham
van1Robert Stedtfeld
van2Robert Stedtfeld
van3Robert Stedtfeld
van4Robert Stedtfeld
van5Robert Stedtfeld
van6Robert Stedtfeld
van7Robert Stedtfeld
van8Robert Stedtfeld
vandSyed Hashsham
vaneSyed Hashsham
vangSyed Hashsham
vanhaSyed Hashsham
vanHBRobert Stedtfeld
vanrbSyed Hashsham
vanRBRobert Stedtfeld
vanrcSyed Hashsham
vanrdSyed Hashsham
vanreSyed Hashsham
van_repARobert Stedtfeld
vanrgSyed Hashsham
vansbSyed Hashsham
vanSBRobert Stedtfeld
vanscSyed Hashsham
vansdSyed Hashsham
vanseSyed Hashsham
vansgSyed Hashsham
vantSyed Hashsham
vanteSyed Hashsham
vantgSyed Hashsham
vanugSyed Hashsham
vanxycSyed Hashsham
vanxyeSyed Hashsham
vanxygSyed Hashsham
vanybSyed Hashsham
vanydSyed Hashsham
vanygSyed Hashsham
vanZRobert Stedtfeld
vataSyed Hashsham
vatbSyed Hashsham
vatcSyed Hashsham
vgbbSyed Hashsham
vphSyed Hashsham
ykkcSyed Hashsham
ykkdSyed Hashsham
ARGs-Resfams
genecontributor
Resfam_16S_Ribosomal_RNA_MethyltransferaseResfam
Resfam_AAC3Resfam
Resfam_AAC3-IaResfam
Resfam_AAC6-IaResfam
Resfam_AAC6-IbResfam
Resfam_AAC6-IIResfam
Resfam_ABCAntibioticEffluxPumpResfam
Resfam_adeA-adeIResfam
Resfam_adeBResfam
Resfam_adeC-adeK-oprMResfam
Resfam_adeRResfam
Resfam_adeSResfam
Resfam_ANTResfam
Resfam_ANT3Resfam
Resfam_ANT4Resfam
Resfam_ANT6Resfam
Resfam_ANT9Resfam
Resfam_APH3Resfam
Resfam_APH3_double_primeResfam
Resfam_APH3_primeResfam
Resfam_APH6Resfam
Resfam_ArmAResfam
Resfam_baeRResfam
Resfam_baeSResfam
Resfam_BCIIResfam
Resfam_BlaBResfam
Resfam_blaIResfam
Resfam_blaR1Resfam
Resfam_CARB-PSEResfam
Resfam_CepAResfam
Resfam_Cfr23RibosomalRNAMethyltransferaseResfam
Resfam_CfxAResfam
Resfam_Chloramphenicol_Acetyltransferase_CATResfam
Resfam_Chloramphenicol_Efflux_PumpResfam
Resfam_Chloramphenicol_Phosphotransferase_CPTResfam
Resfam_ClassAResfam
Resfam_ClassBResfam
Resfam_ClassC-AmpCResfam
Resfam_ClassDResfam
Resfam_CMY-LAT-MOX-ACT-MIR-FOXResfam
Resfam_CTXMResfam
Resfam_DHAResfam
Resfam_DIM-GIM-SIMResfam
Resfam_emrBResfam
Resfam_emrEResfam
Resfam_Erm23SRibosomalRNAMethyltransferaseResfam
Resfam_Erm38Resfam
Resfam_ErmAResfam
Resfam_ErmBResfam
Resfam_ErmCResfam
Resfam_FluoroquinoloneResistantDNATopoisomeraseResfam
Resfam_GESResfam
Resfam_GOBResfam
Resfam_IMPResfam
Resfam_INDResfam
Resfam_KHMResfam
Resfam_KPCResfam
Resfam_L1Resfam
Resfam_LRAResfam
Resfam_macAResfam
Resfam_macBResfam
Resfam_MacrolideGlycosyltransferResfam
Resfam_marAResfam
Resfam_mecR1Resfam
Resfam_MexAResfam
Resfam_MexCResfam
Resfam_MexEResfam
Resfam_MexHResfam
Resfam_MexW-MexIResfam
Resfam_MexXResfam
Resfam_MFSAntibioticEffluxPumpResfam
Resfam_mprFResfam
Resfam_msbAResfam
Resfam_NDM-CcrAResfam
Resfam_norAResfam
Resfam_PC1Resfam
Resfam_phoQResfam
Resfam_QuinoloneResistanceProteinQnrResfam
Resfam_ramAResfam
Resfam_RNDAntibioticEffluxPumpResfam
Resfam_robAResfam
Resfam_romAResfam
Resfam_SfhResfam
Resfam_SHV-LENResfam
Resfam_SMEResfam
Resfam_soxRResfam
Resfam_SPMResfam
Resfam_SubclassB1Resfam
Resfam_SubclassB2Resfam
Resfam_SubclassB3Resfam
Resfam_TE_inactivationResfam
Resfam_TEMResfam
Resfam_TetAResfam
Resfam_TetA-BResfam
Resfam_TetA-GResfam
Resfam_TetDResfam
Resfam_TetEResfam
Resfam_TetH-TetJResfam
Resfam_TetM-TetW-TetO-TetSResfam
Resfam_Tetracycline_Resistance_MFS_Efflux_PumpResfam
Resfam_Tetracycline_Resistance_Ribosomal_Protection_ProteinResfam
Resfam_TetXResfam
Resfam_TetYResfam
Resfam_tolCResfam
Resfam_vanAResfam
Resfam_vanBResfam
Resfam_vanCResfam
Resfam_vanDResfam
Resfam_vanHResfam
Resfam_vanRResfam
Resfam_vanSResfam
Resfam_vanTResfam
Resfam_vanWResfam
Resfam_vanXResfam
Resfam_vanYResfam
Resfam_vanZResfam
Resfam_VEB-PERResfam
Resfam_VIMResfam
Biodegradation
genecontributor
alkbGerben Zylstra/Elyse Rodgers-Vieira
baiCDRDP Staff
benAStephan Gantner
bphGerben Zylstra
bphA1Stephan Gantner
bphA2Stephan Gantner
BSHRobert Stedtfeld
carAShoko Iwai
cntARobert Stedtfeld
cutCRobert Stedtfeld
dbfA1Shoko Iwai
diaAJenny Collier/Alison Cupples
diaA_newJenny Collier/Alison Cupples
dxnAShoko Iwai
dxnA-dbfA1Tim Johnson
etnCHongyu Dang/Alison Cupples
etnEHongyu Dang/Alison Cupples
HSDHRobert Stedtfeld
nfsIJenny Collier/Alison Cupples
npahGerben Zylstra
p450Gerben Zylstra/Elyse Rodgers-Vieira
pnrBJenny Collier/Alison Cupples
ppahGerben Zylstra
PSARobert Stedtfeld
vcrAHongyu Dang/Alison Cupples
vcrA_ver2Hongyu Dang/Alison Cupples
xenAJenny Collier/Alison Cupples
xenBJenny Collier/Alison Cupples
xplAJenny Collier/Alison Cupples
Metal Cycling
genecontributor
ACR3Taylor Dunivin
aioATaylor Dunivin
arrATaylor Dunivin
arsAPFAM
arsBTaylor Dunivin
arsB_oldPFAM
arsCPFAM
arsC_glutTaylor Dunivin
arsC_thioTaylor Dunivin
arsDPFAM
arsMTaylor Dunivin
arxATaylor Dunivin
Other
genecontributor
acdSRDP
cagASyed Hashsham
Cas1_CasYRuonan Wu
Cas1_CasY_nRuonan Wu
Cas1_IBRuonan Wu
Cas1_IB_nRuonan Wu
Cas1_ICIDRuonan Wu
Cas1_ICID_nRuonan Wu
Cas1_IERuonan Wu
Cas1_IE_nRuonan Wu
Cas1_IFRuonan Wu
Cas1_IF_nRuonan Wu
Cas1_IIRuonan Wu
Cas1_I_II_IIIRuonan Wu
Cas1_I_II_III_nRuonan Wu
Cas1_II_nRuonan Wu
Cox1_fungalSiohban Cusack
hcnAThierry Janssens
hlyA.Ezgi YILMAZ
hly_AeromonasA.Ezgi YILMAZ
KS_alpha_PKSIIPatrick Hill
phlDThierry Janssens
phzAThierry Janssens
pltAThierry Janssens
pqsAThierry Janssens
prnDThierry Janssens
RPB1_fungalSiohban Cusack
RPB2_fungalSiohban Cusack
Spo0AJackson Sorenson
TEF1_fungalSiohban Cusack
vacASyed Hashsham
Fungene News

03/05/2018  RDP web tool problems fixed!

03/05/2018  RDP web tool problems
We apologize for ongoing problems with several RDP web tools. Our team is now working hard to get them fixed!

11/10/2017  myRDP login problem fixed!

05/16/2017  Apology for slow/NO connection to RDP tools today
Thanks to Alex/Brian, etc. for working things out in the server room

05/10/2017  RDP Director at GSC 19, May 14-17
Genomic Standards Consortium Meeting, Brisbane, Queensland, Australia

05/10/2017  Possible Friday, May 12, morning interruptions
Emergency Generator Testing from 9-10 A.M.

12/13/2016  Most Highly Cited Researchers
Congratulations to RDP Director James Cole

09/30/2016  RDP Release 11.5 available
Updated 16S rRNA training set to training set No. 16.

08/16/2016  Possible Friday morning interruptions
Building electrical testing/maintenance

06/30/2016  RDP Classifier Updates
The Classifier 16S training set and Fungal ITS Warcup set have been updated

What is the Functional Gene Pipeline/Repository (FGPR)? and other FAQs

  • An interactive display of sequence search results for those interested in a particular gene family.
  • A tool to aid functional genomics studies, especially of the environment; updated monthly.

Where does the search result data come from?

  • FGPR searches are based on a protein model built from a set of different and well characterized "training sequences" submitted by experts.
  • The NCBI non-redundant protein database is searched using the models and the HMMER Hidden Markov Model (HMM) search program. This is the same program used to create the PFAM database of protein motifs.
  • Searches can be repeated using the same models when the protein database is updated.
  • Each gene is searched for common protein motifs using the PFAM database. Scores for these conserved motifs are included in the FGPR output. This can help separate unrelated "hits" that just happen to share a common protein motif with the gene of interest from related but highly diverged sequences.
  • For each "hit" the corresponding protein and nucleic acid records are retrieved. The protein "hits" are aligned using the HMM. Nucleic acid records are aligned by back-translating from the protein alignment. Source organism, reference information, etc. extracted from the records are linked into the FGPR output.

How do HMM searches compare to BLAST?

  • Since HMM models are based on a set of training sequences, they contain much more information than is conveyed by the single query sequence in BLAST. The training set helps define which regions are more conserved and what changes are most common.
  • It's been shown mathematically that the statistical test used in BLAST is essentially equivalent to a type of HMM search with a single training sequence.
  • BLAST is much faster than HMM model searches because it uses a heuristic to filter out sequences unlikely to match.

How do I use the FGPR? (try our new procedural tutorials or our early basic video tutorials*)

  • For each search, you're initially presented with a list of "hits" ordered by score. Starting "training sequences" are presented in color.
  • Jump to the bottom of the list to change the ordering or filter the results based on score, size, or source (environmental clone vs. isolated organisms). Hint: After you've set the filters and ordering to your preference, you can save the page as a "bookmark" in your browser.
  • The score filter is preset to exclude less meaningful results for searches where the total number of results is large. The excluded results can be displayed by changing the filter value.
  • You can choose to display only non-redundant protein hits, or to include redundant entries. (For example, NCBI sometimes considers a well-known training sequence to be a redundant entry if there's an identical protein sequence available.)
  • Protein or nucleic acid alignments can be downloaded for any subset of hits.
  • Analysis tools are being added. Current tools include a neighbor-joining phylogenetic tree builder and a primer/probe tester.

What are the columns in the FGPR display?

  • Select: A checkbox to select the "hit" for download or further analysis.
  • Score: (Bits saved) Score from the HMM search. Directly analogous to the (bits) Score in BLAST.
  • PID, NID: Protein and nucleic acid identifiers with links. NID links are only to the gene coding portion of the nucleic acid record. Some protein hits were not translated from the nucleic acid and do not have a corresponding NID.
  • Definition: From the NCBI protein record.
  • Organism: From the NCBI protein record.
  • Occ.: Occurrence, the number of HMM matches found in the protein. Should normally be 1. Any other number may indicate a false hit.
  • % of HMM Coverage: Percentage of the HMM model that matches the hit protein sequence.
  • % of HMM Identity: Percent identity of the protein sequence that matchs the HMM Model consensus sequence.
  • Size(aa): The length of the protein.
  • Reference: The first reference listed in the NCBI protein record. For those references abstracted by PubMed, a link is provided.
  • Motif(n): Hits are scored against PFAM-A HMMs to common protein motifs present in the gene of interest. Link to the corresponding PFAM records are given at the top of the table.
  • Notes and View/Edit: A place for members to add short notes about a particular "hit."

DOESRP logo linkNIH Human Microbiome Project


References and Support


J.A. Fish, B. Chai, Q. Wang, Y. Sun, C. T. Brown, J. M. Tiedje, and J. R. Cole. (2013). FunGene: the Functional Gene Pipeline and Repository. Front. Microbiol. 4: 291.

A. Bateman, L. Coin, R. Durbin, R.D. Finn, V. Hollich, S. Griffiths-Jones, A. Khanna, M. Marshall, S. Moxon, E.L.L. Sonnhammer, D.J. Studholme, C. Yeats, S.R. Eddy. (2004). The Pfam Protein Families Database. Nucleic Acids Res. Database Issue 32: D138-D141.

D.A. Benson, I. Karsch-Mizrachi, D.J. Lipman, J. Ostell, D.L. Wheeler. (2004). GenBank: update. Nucleic Acids Res. Database issue 32: D23-D26.

R. Durbin, S. Eddy, A. Krogh, G. Mitchison. (1998). The theory behind profile HMMs. In: R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, Biological sequence analysis: probabilistic models of proteins and nucleic acids, Cambridge University Press.