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Phytophthora database 2.0: update and future direction.

TitlePhytophthora database 2.0: update and future direction.
Publication TypeJournal Article
AuthorsPark, B, Martin, F, Geiser, DM, Kim, H-S, Mansfield, MA, Nikolaeva, E, Park, S-Y, Coffey, MD, Russo, J, Kim, SH, Balci, Y, Abad, G, Burgess, T, Grünwald, NJ, Cheong, K, Choi, J, Lee, Y-H, Kang, S
Date Published2013 Dec
Computational Biology, Databases, Genetic, DNA, Mitochondrial, Genotype, Geography, Internet, Microsatellite Repeats, phylogeny, phytophthora, sequence alignment, Sequence Analysis, DNA, Species Specificity

<p>The online community resource Phytophthora database (PD) was developed to support accurate and rapid identification of Phytophthora and to help characterize and catalog the diversity and evolutionary relationships within the genus. Since its release in 2008, the sequence database has grown to cover 1 to 12 loci for &asymp;2,600 isolates (representing 138 described and provisional species). Sequences of multiple mitochondrial loci were added to complement nuclear loci-based phylogenetic analyses and diagnostic tool development. Key characteristics of most newly described and provisional species have been summarized. Other additions to improve the PD functionality include: (i) geographic information system tools that enable users to visualize the geographic origins of chosen isolates on a global-scale map, (ii) a tool for comparing genetic similarity between isolates via microsatellite markers to support population genetic studies, (iii) a comprehensive review of molecular diagnostics tools and relevant references, (iv) sequence alignments used to develop polymerase chain reaction-based diagnostics tools to support their utilization and new diagnostic tool development, and (v) an online community forum for sharing and preserving experience and knowledge accumulated in the global Phytophthora community. Here we present how these improvements can support users and discuss the PD&#39;s future direction.</p>

Citation Key16713
PubMed ID23961810