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.
May 16, 2006
Comparative sequence analysis of B. anthracis Ames Ancestor and a set of diverse B. anthracis strains.
The NIAID sponsored Pathogen Functional Genomics Resource Center (PFGRC) (NIAID contract N01-AI-15447) and the National Science Foundation (NSF Grant 0202304) have funded a study on the comparative sequence analysis of several strains of Bacillus anthracis. The complete genome sequence of B. anthracis Ames Ancestor and high quality draft genome sequence of six diverse B. anthracis strains were determined by whole genome shotgun sequencing. A pipeline was developed (Rasko et al) utilizing MUMmer software to compare, pair wise, the nucleotide sequences of the Ames Ancestor strain with each of the B. anthracis strains in order to identify all single nucleotide polymorphisms (SNPs). In collaboration with the NIAID sponsored Bioinformatics Resource Center (BRC) at TIGR, the comparative SNP data is available here. Note: data not currently available.