2009 IADR, MIAMI, FL, USA Hands-on Experience for using the Human Oral Microbiome Database (HOMD) 2009 IADR Workshop, Miami, FL, USA Tsute (George) Chen

2009 IADR, MIAMI, FL, USA

Hands-on Experience for using the Human Oral Microbiome Database (HOMD)

2009 IADR Workshop, Miami, FL, USATsute (George) Chen

The Forsyth Institute

140 Fenway, Boston, MA, USA


Outline

Introduction Available information and tools

It is more difficult to know what’s available; the how-to is trivial

This slide show can be downloaded on the HOMD web site: http://www.homd.org



Information and Tools

Part I. Basic Web Site Navigation Part II. Taxonomy Part III. Genomics Part IV. Gene Expression with Microarray Part V. Pathway Reconstruction Part VI. Sequence Analysis Tools Part VII. Personal and Community Information

Management


Part I. Navigating the HOMD web site

Menu Help Documentation Search Links










The Meta Search Function







Part II. Taxonomy








Quick link to an HOMD taxon

The numeric taxon ID for Bulleidia extructa is 603, thus to refer to this taxon from a publication or other web sites, use the following URL:

http://www.homd.org/taxon=603




Identification of 16S rRNA sequences

HOMD provides a BLAST search tool for identifying unknown 16S rRNA sequences

The BLAST database contain reference sequences for all categorized human oral taxa

The entire set of reference sequences can be downloaded


Current Statistics of HOMD 16S rRNA Database

Total number of human oral taxa: 619 Total number of 16S rRNA reference sequences: 715 Total number of extended human oral taxa: >1,200* Total number of extended version of 16S rRNA reference

sequence: 1,726 Classified from a total of >34,000 16S rRNA clonal

sequences

* In progress



















Part III. Genomics


Goals of HOMD Genomics Database

To collect genomic sequences of all human oral microorganisms

To provide frequently automatic annotation for important human oral microbial genomes

To provide custom automatic genome annotation for researchers in the oral/dental research community


Features of HOMD Genomic Database

Capable of automatic annotating full (complete), partial (survey), meta (shotgun), and even unassembled trace sequences

Frequent annotation updates (1~2 wks) Automatic metabolic pathway (KEGG) and Gene

Ontology construction Searchable Annotation Annotation information integrated with genomic tools

(e.g., Genome Viewer, Microarray)




Current Statistics of HOMD Genomic Database

Full genomes: 15 Partial (survey) genomes: 19 Meta sequences: 3 Total oral microbial genomes annotated: 37+19 = 56













Part IV. Study gene expression usingmicroarray technology


Comprehensive transcriptome analysis using high-density genomic tiling microarrays




Comprehensive human oral microbial transcriptome database

(under construction)









Comparative Genomics using GOAL

GOAL: Genome-wide ORF Alignment tool Allows comparison of all the ORFs between

two individual genomes Examine common or unique ORFs between

two chosen genomes









Part V. Metabolic pathway and gene ontology reconstructions








Part VI. Sequence analysis with integratedmolecular software package EMBOSS











Part VII. User and community information management features

Storage and management of personal data Use of the EMBOSS molecular software

package Use of the SAOPMD microarray software Personal genomic annotation Participation of curation












HOMD Team and Collaborators



Contact HOMD for Q & A


Acknowledgement

HOMD is supported by the contract U01 DE016937 "A Foundation for the Oral Microbiome and Metagenome" from The National Institute of Dental and Craniofacial Research (NIDCR)

BROP, SAOPMD, myOPMD are supported by the NIDCR grant K22 DE14742.


Documents

2009 IADR, MIAMI, FL, USA Hands-on Experience for using the Human Oral Microbiome Database (HOMD) 2009 IADR Workshop, Miami, FL, USA Tsute (George) Chen