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 7.9 -- GenBank 207 (as of 4/17/2015)
Process your own Functional Gene data using our new FunGene Pipeline

Fungene News

03/27/2015  FrameBot new option Add de novo to references available
Unique abundant query sequences will be added to the starting reference set if qualifications are met.

02/23/2015  WARNING -- RDP unavailable Sat., March 7th
Building network infrastructure upgrades planned 8 A.M. through 6 P.M.

02/16/2015  Introducing Xander assembler
RDP's new gene-target metagenomic assembler, Xander, is released

10/21/2014  Classifier provides gene copy number adjustment
RDP Classifier provides gene copy number adjustment for 16S gene sequences.

09/17/2014  Using RDPTools Output with Phyloseq
A comprehensive tutorial using RDPTools output with Phyloseq package released

09/17/2014  RDP Release 11.3 available
RDP Release 11.3 features updated 16S rRNA hierarchy model

07/08/2014  UNITE Fungal ITS Classifier training set released
Available on RDP Classifier site, RDP SourceForge and GitHub repository.

07/02/2014  BIOM format support
RDP provides support for BIOM format files

07/01/2014  New Warcup Fungal ITS training set released.
Available on RDP Classifier site, RDP SourceForge and GitHub repository.

06/06/2014  RDP staff at MSA meeting, East Lansing MI
Poster about Fungal Analysis

Antibiotic resistances
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
FOXSyed Hashsham
gapATim Johnson
GESSyed Hashsham
IMISyed Hashsham
IMPSyed Hashsham
IncW_trwATim Johnson
IncW_trwBTim Johnson
INDSyed Hashsham
intICarlos Rodriguez-Minguela
intI1_sub1Tim Johnson
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
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
alkbGerben Zylstra/Elyse Rodgers-Vieira
benAStephan Gantner
bphGerben Zylstra
bphA1Stephan Gantner
bphA2Stephan Gantner
carAShoko Iwai
dbfA1Shoko Iwai
dxnAShoko Iwai
dxnA-dbfA1Tim Johnson
npahGerben Zylstra
p450Gerben Zylstra/Elyse Rodgers-Vieira
ppahGerben Zylstra
Biogeochemical cycles
amoA_AOAFeifei Liu
cbh1Cheryl Kuske
chbFan Yang
cooSFan Yang
cydARachel Morris
dsrAAlexander Loy/Michael Wagner
dsrBAlexander Loy/Michael Wagner
exc1Fan Yang
fixNRachel Morris
glxQichao Tu
hydAFan Yang
lcc_ascomycetesChris Wright
lcc_basidiomycetesChris Wright
ligERyan Penton
lipQichao Tu
mcrABlaz Stres
mmoXQichao Tu
mnpQichao Tu
nag3Fan Yang
napALaurent Philippot
narGLaurent Philippot
nirKTracy Teal
nirSVeronica Gruntzig
norBGesche Braker
nosZBlaz Stres
nosZ_atypicalRobert Sanford
nosZ_atypical_1Robert Sanford
nosZ_atypical_2Robert Sanford
nrfAJoel Klappenbach
nrfA_WelshAllana Welsh
phnXZarraz Lee
pmoATracy K. Teal
ppoQichao Tu
soxBGupta Vadakattu
vp1Chris Wright
xylAQichao Tu
Metal Cycling
baiCDRDP Staff
cagASyed Hashsham
hcnAThierry Janssens
phlDThierry Janssens
phoDElizabeth Bent
phzAThierry Janssens
pltAThierry Janssens
pqsAThierry Janssens
prnDThierry Janssens
Spo0AJackson Sorenson
vacASyed Hashsham
Phylogenetic markers
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
avrEJames Kremer

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?

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.