Functional Gene Pipeline and Repository

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find HELP in our video tutorials 


Begin with these gene links:
Version 6.7 -- GenBank (as of 11/24/2011)
Process your own Functional Gene data using our new FunGene Pipeline
Access archived gene files here
Access Fungene 1.0 here

Fungene News

02/10/2012  MSU Network Slowdown
You may experience slow or no connection to the RDP website

12/01/2011  RDP featured in Science Watch, Dec. 2011
Director James Cole answers questions about the RDP Classifier

11/29/2011  Brief Service Interruption
There was a brief power outage from 16:30-17:45 this evening that caused some issues with the RDP sites. The problem has been resolved and all ser...

06/16/2011  RDP User Jobs Slow Turnaround Update
The RDP pyrosequencing site (http://pyro.cme.msu.edu) has been under heavy usage for the past several days (thank you for using our tools!). How...

05/27/2011  RDP Poster at BAGECO11
The RDP FunGene Pipeline: tools for gene-targeted metagenomics

05/18/2011  RDP Staff attending ASM New Orleans, May 22-25
Visit with RDP staff at the poster session on Tues. afternoon

05/04/2011  RDP aids its users in making SRA submissions
Don't have your own submission account? Please call us when you're ready to submit.

05/04/2011  RDP's MIMARKS (former MIENS) GoogleSheets Ready!
Visit our GoogleSheets Help page for further information

04/07/2011  Latest MIMARKS (formerly MIENS) standards released
'The Genomic Standards Consortium: Bringing Standards to Life for Microbial Ecology' is now published online in ISMEJ

04/04/2011  RDP MIMARKS GoogleSheet
RDP developed the MIMARKS GoogleSheet to help you manage the metatdata for your samples.

Antibiotic resistances
genecontributor
cprATamara Tsoi Cole
cprBTamara Tsoi Cole
intICarlos Rodriguez-Minguela
tetMCarlos Rodriguez-Minguela
tetQCarlos Rodriguez-Minguela
tetWCarlos Rodriguez-Minguela
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
bukRDP
butRDP
cooSFan Yang
cydARachel Morris
dsrAAlexander Loy/Michael Wagner
dsrBAlexander Loy/Michael Wagner
fixNRachel Morris
hydAFan Yang
ligERyan Penton
mcrABlaz Stres
napALaurent Philippot
narGLaurent Philippot
nifDRDP
nifHRDP
nifH_titRDP
nirARDP
nirBRDP
nirKGesche Braker
nirSVeronica Gruntzig
norBGesche Braker
nosZBlaz Stres
nrfAJoel Klappenbach
pmoATracy K. Teal
scd2RDP
ureARDP
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
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 video tutorials*)

What are the columns in the FGPR display?

SRP logo link


References and Support

      1R. 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.

      2A. 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. The Pfam Protein Families Database. Nucleic Acids Res. (2004) Database Issue 32:D138-D141.

      3D.A. Benson, I. Karsch-Mizrachi, D.J. Lipman, J. Ostell, D.L. Wheeler. GenBank: update. Nucleic Acids Res. (2004) Database issue 1:D23-6.