Table 1.
Genomics databases and tools available for oral pathogensa
| Organism | Strain | Genome size (Mb) | Collaborating Institute | Funding | Statusb | Databases and tools |
|---|---|---|---|---|---|---|
| Actinobacillus actinomycetemcomitans | HK1651 | 2.90 | University of Oklahoma | NIDCR | 1 | Downloadc: OU |
| BLASTd: OU1, NCBI, BROP, LANL | ||||||
| Databasee: BROP, LANL | ||||||
| Softwaref: BROP, LANL | ||||||
| Actinomyces naeslundii | MG1 | 3 | TIGR | NIDCR | NA | NA |
| Tannerella forsythensis (Bacteroides forsythus) | FDC 92A2 | 3.40 | TIGR | NIDCR | 1 | Download: TIGR1 |
| BLAST: TIGR | ||||||
| Database: TIGR | ||||||
| Software: TIGR | ||||||
| Candida albicans | SC5314 | NA | Stanford Genome Technology Center | NIDCR/Burroughs Wellcome Fund | NA | Download: Stanford |
| BLAST: Stanford | ||||||
| Candida albicans | 1161 | 15 | The Sanger Institute | Beowulf Genomics | NA | Download: Sanger |
| BLAST: Sanger | ||||||
| Fusobacterium nucleatum | ATCC 10953 | 2.4 | Baylor College of Medicine | NIDCR | 101 | Download: BCM |
| BLAST: BCM | ||||||
| Fusobacterium nucleatum | ATCC 25586 | 2.17 | Integrated Genomics | NIH | 1 | Download: IG, NCBI |
| BLAST: NCBI, BROP | ||||||
| Database: LANL BROP | ||||||
| Software: LANL BROP | ||||||
| Fusobacterium nucleatum vincentii | ATCC 49256 | NA | Integrated Genomics | NIH | 302 | Download: IG |
| Porphyromonas gingivalis | W83 | 2.34 | The Forsyth Institute/TIGR | NIDCR | 1 | Download: TIGR2, NCBI |
| BLAST: TIGR, NCBI, BROP, LANL | ||||||
| Database: TIGR, BROP, LANL | ||||||
| Software: TIGR, BROP, LANL | ||||||
| Microarrayg: OPMD | ||||||
| Prevotella intermedia | 17 | 3.8 | TIGR | NIDCR | 1 | Download: TIGR2 |
| BLAST: TIGR | ||||||
| Database: TIGR | ||||||
| Software: TIGR | ||||||
| Streptococcus gordonii (Challis) | NCTC 7868 | NA | TIGR | NIDCR | 273 | Download: TIGR1 |
| BLAST: TIGR | ||||||
| Database: TIGR | ||||||
| Software: TIGR | ||||||
| Streptococcus mitis | NCTC 12261 | 2.2 | TIGR | NIDCR | 1 | Download: TIGR2 |
| BLAST: TIGR | ||||||
| Database: TIGR | ||||||
| Software: TIGR | ||||||
| Streptococcus mutans | UA159 (ATCC 700610) | 2.03 | University of Oklahoma | NIDCR | 1 | Download: OU, NCBI |
| BLAST: OU2, NCBI, BROP, LANL | ||||||
| Database: BROP LANL | ||||||
| Software: BROP LANL | ||||||
| Streptococcus sanguis | SK36 | NA | Virginia Commonwealth University | NIDCR | NA | Download: VCU |
| BLAST: VCU | ||||||
| Streptococcus sobrinus | 6715 | NA | TIGR | NIDCR | NA | Download: TIGR1 |
| Treponema denticola | ATCC 35405 | 2.8 | Baylor College of Medicine/TIGR | NIDCR | 1 | Download: BCM, NCBI |
| BLAST: TIGR, BCM, NCBI, BROP | ||||||
| Database: BROP, LANL | ||||||
| Software: BROP, LANL TIGR | ||||||
| Treponema lecithinolyticum | OMZ 684T | 2.3 | The Forsyth Institute | NIDCR | 1001 | BLAST: BROP |
| Database: BROP | ||||||
| Software: BROP |
aAn up-to-date list is maintained at http://www.brop.org.
bStatus of sequencing is indicated by the number of assembled contigs.
cURLs for sequence download: University of Oklahoma (OU), ftp://ftp.genome.ou.edu/pub; The Institute for Genomic Research (TIGR1), http://www.tigr.org/tigr-scripts/ufmg/ReleaseDate.cgi; The Institute for Genomic Research (TIGR2), ftp://ftp.tigr.org/pub/data/Microbial_Genomes/; Stanford Genome Technology Center (Stanford), http://www-sequence.stanford.edu/group/candida/download.html; The Sanger Institute (Sanger), ftp://ftp.sanger.ac.uk/pub/yeast/sequences/candida; Baylor College of Medicine (BCM), ftp://ftp.hgsc.bcm.tmc.edu/pub/data; Integrated Genomics (IG), http://www.integratedgenomics.com/genomereleases.html and Virginia Commonwealth University (VCU), http://www.sanguis.mic.vcu.edu/.
dURLs for BLAST search tools: OU1, http://www.genome.ou.edu/act_blast.html; OU2, http://www.genome.ou.edu/smutans_blast.html; National Center for Biotechnology Information (NCBI), http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi; Bioinformatics Resource for Oral Pathogens (BROP), http://www.brop.org/modules.php?op=modload&name=News&file=article&sid=10; TIGR, http://tigrblast.tigr.org/ufmg/; Stanford http://www.sequence.stanford.edu/group/candida/search.html; Sanger, http://www.sanger.ac.uk/cgi-bin/blast/submitblast/c_albicans; BCM, http://hgsc.bcm.tmc.edu/microbial/microbialblast.cgi?organism=Fnucleatum and VCU, http://www.sanguis.mic.vcu.edu/.
eURLs for annotation database: BROP, http://genome.brop.org; Los Alamos National Laboratory (LANL), http://www.brop.lanl.gov/ and TIGR, http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl.
fURLs for analysis tools: BROP, http://genome.brop.org; LANL and http://www.brop.lanl.gov.
gURL for microarray database: Oral Pathogen Microarray Database (OPMD), http://array.brop.org.