Annotating Metagenomes Using the SEED Rob Edwards Department of Computer Sciences, San Diego State University Mathematics and Computer Sciences Division,

Annotating Metagenomes Using the SEED

Rob Edwards

Department of Computer Sciences, San Diego State University

Mathematics and Computer Sciences Division, Argonne National Laboratory

NSF/EU Cyberinfrastructure Meeting, Washington, DC.

www.nmpdr.org www.theseed.org

Firstbacterial genome

100bacterial genomes

1,000bacterial genomesN

um

ber

of

know

n s

equence

s

Year

How much has been sequenced?

Environmentalsequencing

Everybody inSan Diego

Everybody inUSA

AllculturedBacteria

100people

How much will be sequenced?

One genome fromevery species

Most majormicrobial environments

What do we want from annotations?

ConsistentAccurateAvailableReliable

www.nmpdr.org www.theseed.org

Consistent

www.nmpdr.org www.theseed.org

The Importance of Consistency

• Consistency: same genes connected to same functional role

• Enables communication

• Required for most comparative genomics assays

www.nmpdr.org www.theseed.org

hisAFIG function:

Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16)

Other functions in RefSeq:

phosphoribosylformimino-5-aminoimidazole carboxamidephosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerasephosphoribosylformimino-5-aminoimidazole carboxamide ribotide...

1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase

N-(5-phospho-L-ribosyl-formimino)-5-amino-1-(5- phosphoribosyl)-4-imidazolecarboxamide isomeraseN-(5'-phospho-L-ribosyl-formimino)-5-amino-1-(5'-phosphoribosyl)-4-imidazolecarboxamide isomeraseN-(5'-phospho-L-ribosyl-formimino)-5-amino-1- (5'- phosphoribosyl)-4-imidazolecarboxamide isomeraseN-(5'-phospho-L-ribosyl-formimino)-5-amino-1- (5'-phosphoribosyl)-4-imidazolecarboxamide isomeraseN-(5'-phospho-L-ribosyl-formimino)-5-amino-1- (5'-phosphoribosyl)-4- imidazolecarboxamide isomerase

Phosphoribosyl isomerase A [1-[5-phosphoribosyl]-5-[[5-phosphoribosylamino]methylideneamino] imidazole-4-carboxamide isomerase]

www.nmpdr.org www.theseed.org

Measuring Consistency• Define a set of protein families such that each family

contains genes playing the same function

• Attach functional roles to protein families• Measure the consistency of the annotations made to

genes within each family

1. "consistency" is the odds that two proteins from the same family have the same function

2. Evaluate both families and functions.

www.nmpdr.org www.theseed.org

Consistency among databases

www.nmpdr.org www.theseed.org

Accurate

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How to measure accuracy

• If everything was called “hypothetical protein” the database would be 100% consistent

• Need to measure accuracy (specificity) as well as consistency

• Sample 100 proteins at random from “curated” set (i.e. that are believed to be correct)

• Manually inspect annotations to score correctness

www.nmpdr.org www.theseed.org

Available

www.nmpdr.org www.theseed.org

http://metagenomics.theseed.org

Free serviceUser registration/log inFree to upload sequences in several formatsAutomatically annotates sequencesDownload in several formats

Complete genomes too: http://www.nmpdr.org/anno-server

Soon to come:Plasmids, phages, other short genomes

Metagenome Metabolic Reconstruction

Metabolic potential in environments

Phylogenomics

Comparing Metagenomes to Genomes(or other metagenomes!)

Reliable (Believable)

Metabolic potential in environments

Sulfur

CDA 60.2%

CD

A 2

1.7

% Respiration

Capsule Motility

Membranetransport

Stress

Signaling

Phosphorus

RNA

MineSaltern

MarineMicrobialites

CoralFish

AnimalsFreshwater

From sequences to environments

What do we want from annotations?

ConsistentAccurateAvailableReliable

When

do

we wan

t it?

NOW

AcknowledgementsEnvironmental Genomics

Forest RohwerRohwer lab membersAll the labs that

provided sequence

Metagenomics Annotation ServerRick StevensDaniel Paarman Folker MeyerBob Olsen

StatisticsLiz DinsdaleDana HallBeltran Rodriguez-Brito

FIGRoss OverbeekVeronika VonsteinAnnotators

Subsystems make up metabolism

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