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Comparative genome

Pyrococcus horikoshii OT3T (= NBRC 100139T)


reference genomedotplotortholog listcomparative map
Pyrococcus abyssi GE5ListMap
Pyrococcus furiosus DSM 3638ListMap
Thermococcus kodakaraensis KOD1ListMap

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We analyzed the relationships among all genes/ORFs in the four archaeal genomes and the results were incorporated into the DOGAN.
You can compare genes/ORFs in the genomes listed bellow and get the syntenic regions or points of possible genomic rearrangements displayed in the dotplot viewer. In addition, we provide you with lists of putative orthologs ordered by their genomic locations, with which you may see, for example, if the target genes/ORFs of your interest exist in an operon are well conserved amongst the related species, etc.


Target genomes
We prepared comparative genomics data for the following hyperthermophilic archaea, all belong to the Thermococcaceae family (note that this analysis does not include ORFs of plasmids.)

Pyrococcus horikoshii OT3T (NITE)
This is the first organism whose genome was analyzed at NITE.

Pyrococcus abyssi GE5
Pyrococcus furiosus DSM 3638
Thermococcus kodakarensis KOD1
The ORFs annotated in these genomes were extracted from the NCBI RefSeq (Reference Sequence) and incorporated into the DOGAN as reference data.

Analytical criteria
Computational analysis was performed based on the following criteria.


Homologs

ORFs of P.horikoshii, P.abyssi, P.furiosus and T.kodakarensis were classified into mutually homologous groups.


ORFs with more than 50 BLAST bit score and 60% "quality ratio" (coverage) values reported by the NCBI-BLAST (blastp program) were classified together to form a homolog group.
The data may be helpful to find ORFs of other species that show similarities with your targets.

A paralogous group was subsequently defined as a homology group that contains more than one ORF derived from a single genome.

Orthologs

For each group of homology, orthologous ORFs were predicted by bidirectional best hits when ORF X of a genome shows highest similarity of all genes of the genome with ORF Y of another genome used as query and vice versa, according to the results obtained by running the blastp program.
We have prepared a list of putative orthologous ORFs of the genomes listed above. You can see the list sorted by gene order of the target genome of your interest.