Comparison between HOMD and LANL ORALGEN Annotated Genomes

Genome Name HOMD/NCBI
Genome Information
ORALGEN
Genome Information
Has Oralgen Annotation Panel
in HOMD JBrowse?
Other Info
Contigs/
Molecules
Combined
Size (bps)
Contigs/
Molecules
Combined
Size (bps)
Actinomyces naeslundii MG1 1 3,042,856 1 3,042,856  YES  FTP *
Fusobacterium nucleatum ATCC 25586 ** 1 2,174,500 4 2,192,643  YES  FTP *
Porphyromonas gingivalis ATCC 33277 1 2,354,886 1 2,354,886  YES  FTP *
Porphyromonas gingivalis W83 * 1 2,343,476 1 2,343,479  YES  FTP *
Prevotella intermedia 17 # 2 2,699,437 3 2,135,969  YES  FTP *
Streptococcus gordonii Challis substr. CH1 1 2,196,662 1 2,196,662  YES  FTP *
Streptococcus mitis NCTC 12261 1 2,045,857 1 2,045,857  YES  FTP *
Streptococcus sanguinis SK36 1 2,388,435 1 2,388,435  YES  FTP *
Treponema denticola ATCC 35405 ## 1 2,843,201 2 2,846,850  YES  FTP *
Aggregatibacter actinomycetemcomitans HK1651
(Actinobacillus actinomycetemcomitans HK1651)
1 2,105,332 2 2,130,910  NO  FTP * *
Fusobacterium nucleatum subsp. polymorphum ATCC 10953
(Fusobacterium nucleatum polymorphum)
14 2,428,298 2 2,441,532  NO  FTP * *
Streptococcus mutans UA159 1 2,032,925 8 2,088,156  NO  FTP * *
Tannerella forsythia ATCC 43037 1 3,405,521 5 3,505,077  NO  FTP * *
* The Porphyromonas gingivalis W83 genomic sequence annotated by ORALGEN has the following 3 additional nucleotides. Although for convenience, we still provide an ORALGEN panel in the HOMD JBrowse (above) for this genome, please note that the coordination for the ORALGEN annotated genes will be 1,2 or 3 bases off when aligned to the HOMD genome:
479,441 bp
NCBI:    G-CCT
Oralgen: GNCCT

880,452 bp
NCBI:    C-TTT
Oralgen: KYYTT

1,138,113 bp
NCBI:    A-AATT
Oralgen: ANAATT
** ORALGEN recorded 3 plasmids (pFN1,pKH9,pPA52) which NCBI does not have.
# In addition to the two chromosomes, ORALGEN has an additional sequence for plasmid pYHBi1.
## ORALGEN recorded a plasmid pTS1 which NCBI does not have.
* This FTP folder contains all the original ORALGEN data exported to Excel spread sheets
* Since the genomic sequences annotated by ORALGEN is different from the current updated genomic sequences annotated by HOMD, we provide a Oralgen gene ID => HOMD/NCBI gene ID mapping table based on the BLAST Search Result. In the provided FTP folder, please look for a file named either:

lanl_gene_id_2_ncbi_blastp.csv
or
lanl_gene_id_2_homd_blastp.csv
   ~ Contact George Chen (electronic mail: tchen at forsyth.org) if there's any question ~


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