Functional Gene Pipeline / Repository

What is the Functional Gene Pipeline/Repository (FGPR)?
New Video Tutorials

Begin with these gene links:

Version 5.7 -- GenBank Rel. 173.0 (as of 11 Sept '09)
Access archived gene files here

Antibiotic resistances		Biodegradation
gene	contributor	gene	contributor
intI	Carlos Rodriguez-Minguela	benA	Stephan Gantner
tetM	Carlos Rodriguez-Minguela	bph	Gerben Zylstra
tetQ	Carlos Rodriguez-Minguela	bphA1	Stephan Gantner
tetW	Carlos Rodriguez-Minguela	bphA2	Stephan Gantner
		cprA	Tamara Tsoi Cole
		cprB	Tamara Tsoi Cole
		npah	Gerben Zylstra
		ppah	Gerben Zylstra

Biogeochemical cycles		Phylogenetic markers
gene	contributor	gene	contributor
pmoA	Pfam	fusA	Scott Santos/Howard Ochman
butyryl CoA:acetate CoA transferase		gyrB	Zarraz May-Ping Lee
dsrA	Alexander Loy/Michael Wagner	ileS	Scott Santos/Howard Ochman
dsrB	Alexander Loy/Michael Wagner	lepA	Scott Santos/Howard Ochman
dsrA_dsrB	Alexander Loy/Michael Wagner	leuS	Scott Santos/Howard Ochman
mcrA	Blaz Stres	pyrG	Scott Santos/Howard Ochman
napA	Laurent Philippot	recA	Scott Santos/Howard Ochman
nifH	Ederson Jesus	recG	Scott Santos/Howard Ochman
narG	Laurent Philippot	rplB	Scott Santos/Howard Ochman
nirK	Gesche Braker	rpoB	Scott Santos/Howard Ochman
nirS	Veronica Gruntzig
norB	Gesche Braker
nosZ	Blaz Stres
nrfA	Joel Klappenbach
pmoA	Tracy K. Teal

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 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 Match: Percentage of the HMM model that matches the hit protein 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."

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.