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.

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DNA Microarrays

The PFGRC designs, constructs, and distributes 70-mer glass slide DNA microarrays for pathogens and biodefense related organisms (Select A-C agents), and the NIAID solicits applications on an ongoing basis from investigators world-wide seeking access to the PFGRC DNA microarray resource. In addition, the PFGRC and NIAID, in collaboration with the NIDCR, also provide access to several dental pathogen microarrays. The 39 microarrays currently supported by the PFGRC are listed here. The NIAID and PFGRC provide these microarrays at no cost to approved investigators. Application instructions can be found on the NIAID and NIDCR websites. All approved investigators must complete an MTA in order to receive their allotment of microarrays.

The PFGRC offers several valuable resources and reagents to the scientific community in support of DNA microarray research. The resource descriptions below provide links to their location and availability on the PFGRC website.

Project Description / Publications

Reagents and Resources

Collaborators

DNA Microarray Reagents

Microarrays and Annotation Files, FAQs, and SOPs

Identification of competence pheromone responsive genes in Streptococcus pneumoniae by use of DNA microarrays

The PFGRC Test Array

Don Morrison, University of Illinois, Chicago

Universal microarray standard probe set

The PFGRC Universal Microarray Standard Probe Set