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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)

2009 IADR Workshop, Miami, FL, USA

Tsute (George) Chen

The Forsyth Institute

140 Fenway, Boston, MA, USA

2009 IADR, MIAMI, FL, USA

outline
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

information and tools
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

part i navigating the homd web site
Part I. Navigating the HOMD web site
  • Menu
  • Help Documentation
  • Search
  • Links

2009 IADR, MIAMI, FL, USA

the meta search function
The Meta Search Function

2009 IADR, MIAMI, FL, USA

part ii taxonomy
Part II. Taxonomy

2009 IADR, MIAMI, FL, USA

quick link to an homd taxon
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

identification of 16s rrna sequences
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

current statistics of homd 16s rrna database
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

part iii genomics
Part III. Genomics

2009 IADR, MIAMI, FL, USA

goals of homd genomics database
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

features of homd genomic database
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)

2009 IADR, MIAMI, FL, USA

current statistics of homd genomic database
Current Statistics of HOMD Genomic Database
  • Full genomes: 15
  • Partial (survey) genomes: 19
  • Meta sequences: 3
  • Total oral microbial genomes annotated: 37

+19 = 56

2009 IADR, MIAMI, FL, USA

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Comprehensive transcriptome analysis using

high-density genomic tiling microarrays

2009 IADR, MIAMI, FL, USA

comprehensive human oral microbial transcriptome database under construction
Comprehensive human oral microbial transcriptome database(under construction)

2009 IADR, MIAMI, FL, USA

comparative genomics using goal
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

2009 IADR, MIAMI, FL, USA

part vi sequence analysis with integrated molecular software package emboss
Part VI. Sequence analysis with integratedmolecular software package EMBOSS

2009 IADR, MIAMI, FL, USA

part vii user and community information management features
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

2009 IADR, MIAMI, FL, USA

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HOMD Team and Collaborators

2009 IADR, MIAMI, FL, USA

slide116

Contact HOMD for Q & A

2009 IADR, MIAMI, FL, USA

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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.

2009 IADR, MIAMI, FL, USA