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.
December 4, 2007
The PFGRC and Harvard Institute of Proteomics Announce the Availability of a second Bacillus anthracis Gateway® Entry Clone Set
The National Institute of Allergy and Infectious Diseases (NIAID) sponsored Pathogen Functional Genomics Resource Center (PFGRC) at JCVI is pleased to announce the addition of a second Bacillus anthracis strain Ames clone set to the PFGRC Gateway® Entry Clone Resource. This B. anthracis ORFeome library was prepared and full-length sequence verified by the Harvard Institute of Proteomics with support from NIAID. This new B. anthracis clone collection consists of 5175 validated open reading frames constructed in the pDONR221 Invitrogen Gateway® Entry Clone Vector with modified att sites. Unlike the original B.anthracis Ames clone set constructed by the PFGRC in May 2004, the native stop codons are absent from these cloned ORFs. The PFGRC is making this resource available to the research community free of charge as a complete clone set or individual entry clones. Please follow the link to the PFGRC Invitrogen Gateway® Entry Clone Resource for detailed ordering instructions for the complete clone set or individual clones.