Influenza research database: an integrated bioinformatics resource for influenza research and surveillance.
Bottom Line: IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature.To demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented.A comparison of hemagglutinin sequence conservation and epitope coverage information revealed highly conserved protein regions that can be recognized by the human adaptive immune system as possible targets for inducing cross-protective immunity.
Affiliation: Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.Show MeSH
Related in: MedlinePlus
License 1 - License 2
Mentions: The IRD supports numerous analysis tools, including the inference of maximum-likelihood phylogenetic trees using PhyML.41 A user can select a quick version of tree inference using default PhyML settings or specify the PhyML settings themselves. If the user does not know the best settings for PhyML for a particular set of sequences, the IRD custom software, ModelCompare, can be run to compare the fit of these data to a range of different models of evolution. The IRD also provides a customized tree viewer based on Archaeopteryx (http://www.phylosoft.org/archaeopteryx)42 that incorporates Archaeopteryx functions, such as re-rooting, subtree ordering, and branch swapping in addition to allowing the user to decorate the tree labels based on sequence metadata characteristics including subtype, host, country, or year of isolation derived from the IRD database (Figure 3).
Affiliation: Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.