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

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. Outline. Introduction Available information and tools

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

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  1. 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 2009 IADR, MIAMI, FL, USA

  2. 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 2009 IADR, MIAMI, FL, USA

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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 2009 IADR, MIAMI, FL, USA

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

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  14. The Meta Search Function 2009 IADR, MIAMI, FL, USA

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  20. Part II. Taxonomy 2009 IADR, MIAMI, FL, USA

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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 2009 IADR, MIAMI, FL, USA

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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 2009 IADR, MIAMI, FL, USA

  31. 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 2009 IADR, MIAMI, FL, USA

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  49. Part III. Genomics 2009 IADR, MIAMI, FL, USA

  50. 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 2009 IADR, MIAMI, FL, USA

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