Three New Bioinformatics Tools Available
The NIAID sponsored Pathogen Functional Genomics Resource Center (PFGRC) at the J. Craig Venter Institute is pleased to announce the release of three new, free open-source software tools: Magnolia, Ginkgo and APEX. Magnolia is a microarray data management and export system for researchers who use PFGRC microarrays. The software greatly simplifies the tasks of organizing experimental data and submitting it to a public data repository. Ginkgo is a Comparative Genomic Hybridization (CGH) and expression microarray data analysis package. Several normalization, data filtering and imputation, and replicate microarray functions are implemented in an intuitive graphical framework. The APEX tool is an implementation of the Absolute Protein Expression quantitation technique. It can compute protein abundance values for LC-MS/MS proteomics datasets, quantifying hundreds or thousands of proteins. Links to additional information on each of these new software tools is available from the PFGRC's bioinformatics page.
Microarray Suggestion Criteria
The National Institute of Allergy and Infectious Diseases (NIAID) supported Pathogen Functional Genomics Resource Center (PFGRC) designs, constructs, and distributes glass slide DNA microarrays for pathogens and biodefense related organisms (Select A-C agents). Currently, the PFGRC supports DNA microarrays for the 38 organisms listed here. In continuing its efforts to provide the infectious disease and biodefense communities with the microarray resources most relevant to their research efforts, the PFGRC is soliciting input for selection of its next set of reference/species microarrays. The criteria for organism selection may be found here.
July 13, 2007
The PFGRC announces three new microarrays available for distribution
The National Institute of Allergy and Infectious Diseases (NIAID) sponsored Pathogen Functional Genomics Resource Center (PFGRC) at the J. Craig Venter Institute (JCVI) announces the addition of three new glass slide microarray resources, Streptococcus pyogenes, Streptococcus sanguinis and a Haemophilus influenzae species array, to its DNA microarray collection. The S. pyogenes microarray design is described in detail here. It consists of 9,445 unique oligos designed from 11 sequenced strains and the plasmid pDN571. The S. sanguinis micorarray design is based on the 2,348 ORFs from the sequenced strain SK36 (see here), and is supported through generous funding from the National Institute of Dental and Craniofacial Research (NIDCR). The H. influenzae species DNA microarray design consists of 4,454 oligos and is based on available sequence information from five strains (Rd KW20, 86-028NP, R2846, R2866, HK1212), two plasmids (pF3028, pF3031) and one genetic island (F3031). A detailed description of the microarray can be found here. We highly recommend that this microarray be used for carrying out comparative genomics investigations. Details with respect to the application process and review criteria for obtaining all PFGRC supported microarrays can be found at the NIAID PFGRC web site.