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.
August 16, 2006
Comparative sequence analysis of S. pneumoniae TIGR 4 and a set of diverse S. pneumoniae strains.
The NIAID sponsored Pathogen Functional Genomics Resource Center (PFGRC) (NIAID contract N01-AI-15447) has funded a study on the evaluation of resequencing oligonucleotide array technology to detect genotypic variations in microorganisms. The PFGRC, in collaboration with Dr. Catherine McEllistrem, Division of Infectious Diseases, The University of Pittsburg, has evaluated Affymetrix CustomSeq Resequencing Oligonucleotide Array technology to detect genotypic variations in 85 S. pneumoniae isolates. A detailed description of the study may be found here and the data presentation may be found here, including a detailed, interactive SNP report providing comparative analyses between the TIGR 4 strain and any grouping of the S. pneumoniae isolates.