Isobase specifications


Unique identifier OMICS_04891
Name Isobase
Alternative name IsoRank PPI Network Alignment Based Ortholog Database
Restrictions to use None
Maintained Yes


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Publication for IsoRank PPI Network Alignment Based Ortholog Database

Isobase citations


PlantOrDB: a genome wide ortholog database for land plants and green algae

BMC Plant Biol
PMCID: 4481079
PMID: 26112452
DOI: 10.1186/s12870-015-0531-4

[…] gID, do not allow users to browse and retrieve all gene families and their search capabilities are very limited. Some databases do not permit users to upload their query sequences for analysis (e.g., Isobase and PhylomeDB) or provide a very preliminary BLAST report for the query sequences (e.g., CEG, PLAZA 3.0, EnsemblPlants and Inparanoid8). Some databases have rudimentary, less interactive web i […]


Accurate multiple network alignment through context sensitive random walk

BMC Syst Biol
PMCID: 4331682
PMID: 25707987
DOI: 10.1186/1752-0509-9-S1-S7

[…] INALOG was excluded as the algorithm can only handle pairwise alignments. For IsoRankN, we set the parameter α to 0.6 as in the original paper []. For BEAMS, we set the filtering threshold to 0.4 for IsoBase and 0.2 for NAPAbench as in the original paper [], and set the parameter α to 0.5. The parameter α for NetCoffee was set to 0.5. We used default parameters for SMETANA (i.e., nmax = 10, α = 0. […]

Isobase institution(s)
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA

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