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 7.4 -- GenBank 199 (as of 12/13/2013)
Process your own Functional Gene data using our new FunGene Pipeline

Fungene News

03/26/2014  Informatics Professional job opening at RDP
Work with a team developing important bioinformatics resources.

03/19/2014  All services should be back online!
Sorry for the interruption.

03/19/2014  RDP Site Issues
Some services temporarily unavailable.

03/07/2014  RDP Release 11.2
RDP Release 11.2 features updated Fungal 28S LSU hierarchy model

11/08/2013  Fungene Repository Release 7.3
Release 7.3 of the Functional Gene Repository is now live at http://fungene.cme.msu.edu/. This release includes a new gene, nxrB, and updated with ...

10/16/2013  RDP 11 and RDPipeline are now live
RDP 11 and the new RDP Pipeline for Amplicon Sequences (RDPipeline) are now live and available to researchers.

10/16/2013  RDP 11 Major Release Tonight
RDP sites will be down this evening for new release deployment

10/09/2013  FunGene article published
The article describing our FunGene data and tools is published in Frontier in Microbiolgy.

10/09/2013  RDP FrameBot article published
The article describing RDP FrameBot (a frameshift correction tool) is published in the journal mBio

10/01/2013  RDP Staff and Poster
5th Argonne Soil Metagenomics Meeting

Antibiotic resistances
genecontributor
beta_IS6Robert Stedtfeld
beta_tnpARobert Stedtfeld
beta_tnpA2Robert Stedtfeld
bet_blaSHVRobert Stedtfeld
bet_tnpARobert Stedtfeld
cefa_qacEdeltaRobert Stedtfeld
chl_cmlARobert Stedtfeld
cprATamara Tsoi Cole
cprBTamara Tsoi Cole
dfra1Syed Hashsham
dfra12Syed Hashsham
gapATim Johnson
IncW_trwATim Johnson
IncW_trwBTim Johnson
intICarlos Rodriguez-Minguela
intI1_sub1Tim Johnson
intI2Tim Johnson
intI3Tim Johnson
mdh_sub1Tim Johnson
mdh_sub2Tim Johnson
pec_aad2Robert Stedtfeld
repATim Johnson
spec_aad1Robert Stedtfeld
strARobert Stedtfeld
strBRobert Stedtfeld
strept_aadRobert Stedtfeld
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
Biodegradation
genecontributor
alkbGerben Zylstra/Elyse Rodgers-Vieira
benAStephan Gantner
bphGerben Zylstra
bphA1Stephan Gantner
bphA2Stephan Gantner
carAShoko Iwai
dbfA1Shoko Iwai
dxnAShoko Iwai
dxnA-dbfA1Tim Johnson
glxQichao Tu
lipQichao Tu
mmoXQichao Tu
mnpQichao Tu
npahGerben Zylstra
p450Gerben Zylstra/Elyse Rodgers-Vieira
ppahGerben Zylstra
ppoQichao Tu
xylAQichao Tu
Biogeochemical cycles
genecontributor
amoARDP
amoA_AOAFeifei Liu
bukRDP
butRDP
cbh1Cheryl Kuske
chbFan Yang
cooSFan Yang
cydARachel Morris
dsrAAlexander Loy/Michael Wagner
dsrBAlexander Loy/Michael Wagner
exc1Fan Yang
fixNRachel Morris
hydAFan Yang
lcc_ascomycetesChris Wright
lcc_basidiomycetesChris Wright
ligERyan Penton
mcrABlaz Stres
nag3Fan Yang
napALaurent Philippot
narGLaurent Philippot
nifDRDP
nifHRDP
nirARDP
nirBRDP
nirKTracy Teal
nirSVeronica Gruntzig
norBGesche Braker
nosZBlaz Stres
nrfAJoel Klappenbach
nrfA_WelshAllana Welsh
nxrBRDP
phnXZarraz Lee
pmoATracy K. Teal
scd2RDP
soxBGupta Vadakattu
ureARDP
vp1Chris Wright
Metal Cycling
genecontributor
arsAPFAM
arsBPFAM
arsCPFAM
arsDPFAM
Other
genecontributor
hcnAThierry Janssens
phlDThierry Janssens
phzAThierry Janssens
pltAThierry Janssens
pqsAThierry Janssens
prnDThierry Janssens
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
rpoBScott Santos/Howard Ochman
Plant Pathogenicity
genecontributor
avrEJames Kremer
txtARDP
txtBRDP

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

Where does the search result data come from?

How do HMM searches compare to BLAST?

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

What are the columns in the FGPR display?

SRP logo link


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.