1. 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 The Forsyth Institute 140 Fenway, Boston, MA, USA

2. 2009 IADR, MIAMI, FL, 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

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4. 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

5. 2009 IADR, MIAMI, FL, USA Part I. Navigating the HOMD web site Menu Help Documentation Search Links

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14. The Meta Search Function

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20. Part II. Taxonomy

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27. 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

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30. 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

31. 2009 IADR, MIAMI, FL, USA 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

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49. Part III. Genomics

50. 2009 IADR, MIAMI, FL, USA 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

51. 2009 IADR, MIAMI, FL, USA 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)

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54. Current Statistics of HOMD Genomic Database Full genomes: 15 Partial (survey) genomes: 19 Meta sequences: 3 Total oral microbial genomes annotated: 37 +19 = 56

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66. Part IV. Study gene expression using microarray technology

67. 2009 IADR, MIAMI, FL, USA Comprehensive transcriptome analysis using high-density genomic tiling microarrays

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70. Comprehensive human oral microbial transcriptome database (under construction)

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78. 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

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86. Part V. Metabolic pathway and gene ontology reconstructions

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93. Part VI. Sequence analysis with integrated molecular software package EMBOSS

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103. 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

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114. HOMD Team and Collaborators

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116. Contact HOMD for Q & A

117. 2009 IADR, MIAMI, FL, USA 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.

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