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Bioinformatics Challenges in Data Handling and Presentation to the Bioinformaticists

Metagenomic nucleotide sequence and annotation: Range of environments

Global ocean survey

Human faecal virus communities

Human distal gut microbiome

Phosphorus removal sludge communities

Obesity-associated gut microbiome

Acidophilicbacterial community

Mouse gut flora

Metagenomic nucleotide sequence and annotation: Data growth: projects

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Metagenomic nucleotide sequence and annotation: Data growth: volume of dataset

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Metagenomic nucleotide sequence and annotation: Assembly issues

Most metagenome records have not been assembled into scaffolds in INSDC records (only 4 of 24 projects so far) and remain as unassembled WGS records

Those that have been assembled into scaffolds show very limited assembly - of the four assembled projects, one contains almost as many scaffolds as contigs

Metagenomic nucleotide sequence and annotation: Metadata issues

• Metadata, particularly sampling information, are often not shown, or are provided with limited granularity, restricting re-analysis by users

• INSDC offers appropriate structures for such metadata, but they are frequently not used, even when the information is available to the submitters

Current:FT source 1..2866FT /organism="marine metagenome"FT /environmental_sampleFT /mol_type="genomic DNA"FT /isolation_source="isolated as part of a large datasetFT composed predominantly from surface water marine samplesFT collected along a voyage from Eastern North American coastFT to the Eastern Pacific Ocean, including locations in theFT Sargasso Sea, Panama Canal, and the Galapagos Islands"FT /note="metagenomic"FT /db_xref="taxon:408172"

Could be:FT source 1..2866FT /organism="marine metagenome"FT /environmental_sampleFT /mol_type="genomic DNA"FT /country="French Polynesia: Moorea, Cooks Bay"FT /lat_lon="17.476 S 149.81 W"FT /isolation_source="marine surface water; sampleFT depth: 34M; size range: 0.1-0.8 microns; waterFT temperature: 28.900; salinity: 35.100"FT /db_xref="taxon:408172"

Metagenomic nucleotide sequence and annotation: Taxonomy issues

Taxonomic annotation in metagenomic data is simplistic - a very small number of non-specific taxa are necessarily used to describe all of the raw data

Analysis methodology, particularly binning, is inconsistent across the dataset, so taxonomic assertions in assembled sequence are of uncertain provenance

Standards on whether or not single contigs should contribute to scaffolds for more than one taxon are yet to be established

Metagenomes and UniProt (1/2)

• As of this month, ~6 million protein sequences from Global Ocean Survey have been released (vs. 4,534,260 UniProtKB entries)

• Future exponential increase is anticipated:• The growth of public protein sequence data is exponential with a

doubling time of about 20 months• Metagenomics data will have substantially shorter doubling time• GOS data will more than double the existing protein-coding

sequences in UniProtKB

Metagenomes and UniProt (2/2)

• Perspectives• Vast amount of sequence data• Environmental context in metadata• New kind of data requires new storage, processing, and data mining

procedures

• Taxonomically unassigned data will not be included in the UniProt Knowledgebase

• UniMES – UniProt Metagenomics and Environmental sequences (June 2007)

UniMes requirements

• Distinct storage and dissemination: separated from current UniProt databases.

• Distinct production pipeline• Distinct accession number range: MES followed by 11

hexadecimal numbers, e.g. MES00000000001• Distinct data mining pipelines: less restricted rules due to

the lack of basic knowledge about the taxonomic origin of these sequences

UniMes pipeline overview

EMBL

Primary data

Genomic sequence (EMBL)

Other SubmissionsMetagenomics data

(WGS)

UniProt KnowledgebaseUniProt Metagenomics UniProt Archive

Classification

Clustering

Automatic annotationrules

Secondary analysis

Secondary analysis

DNA Metagenomics (to be established)

UniProtKB vs.UniMes Database growth

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2005 2006 2007

UniProt Knowledgebase (in mln of sequences)UniProt Metagenomics and Environmental Sequences (in mln of sequences)

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2005 2006 2007

UniProt Metagenomics and Environmental Sequences (storage in GB)

UniMes storage growth

UniMes hardware requirements (1/2)

• 2 HP/Compaq AlphaServers ES45 with 4 1250MHz CPU’s and 12GB Memory

Oracle database designed to store and maintain data

derived from EMBL

Oracle Warehouse for data analysis, integration

and display

• 64-bit linux farm (AMD operon) using 40 nodes for data mining procedures

UniMes hardware requirements (2/2)

• New oracle servers: Sunfire v490 with 4 1500MHz UltraSparc IV CPUS’s and 16 GB memory

• We have enough physical storage and CPU power for 2007

UniMes dissemination

• FASTA and XML files• UniProt Web Site: text and similarity searches

GOS submission

• Submission of nucleic acid sequence data to EMBL/GenBank/DDBJ is mandatory for publication of scientific paper

• Craig Venter Institute submission to EMBL/GenBank/DDBJ in March 2007

• Environmental metadata can only be found in the CAMERA website

• Metadata are of great importance for metagenomic sequence data:• Descriptions of sampling sites and habitats • Analysis of metagenomics sequence data

• URGENT need for the community to agree on what metadata must be included with the submission of any metagenomics sample

UniMes and GOS data

Protein Sequences

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GOS UniParc

Amino Acids (bln)

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GOS UniParc

Average Sequence Length

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GOS UniProt KB

Median Sequence Length

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GOS UniProt KB

UniMes and GOS data

Fragm ents (%)

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GOS UniP rot KB

Amino Acid Distribution

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A R N D C Q E G H I L K M F P S T W Y V B Z X

GOS UniProt KB

UniMes and GOS data

Percentage Coverage by InterPro Methods

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81.5

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82.5

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UniProt KB UniParc GOS

UniMes and GOS data

Top 10 InterPro entries hitting UniProt: Top 10 InterPro entries hitting GOS

Top 10 InterPro entries hitting UniParc (including GOS):

UniMes and GOS data: Analysis

Calculation time: 763,425 CPU hoursStorage for InterPro hits to GOS: 50 GB