2009 IADR, MIAMI, FL, USA Hands-on Experience for using the Human Oral Microbiome Database (HOMD)...
Transcript of 2009 IADR, MIAMI, FL, USA Hands-on Experience for using the Human Oral Microbiome Database (HOMD)...
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
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
2009 IADR, MIAMI, FL, USA
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
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
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
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
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
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
Full genomes: 15 Partial (survey) genomes: 19 Meta sequences: 3 Total oral microbial genomes annotated: 37+19 = 56
2009 IADR, MIAMI, FL, USA
Comprehensive transcriptome analysis using high-density genomic tiling microarrays
2009 IADR, MIAMI, FL, USA
Comprehensive human oral microbial transcriptome database
(under construction)
2009 IADR, MIAMI, FL, USA
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 integratedmolecular software package EMBOSS
2009 IADR, MIAMI, FL, USA
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
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.