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.
Bioinformatic SNP Filter Scripts
Scripts for Filtering Raw SNP calls from Affymetrix GeneChip® Resequencing Chips
We have developed a set of scripts to identify and remove false positive SNP calls that are present in the CHP files produced by the Affymetrix GSEQ software. These scripts are described in an online presentation available here, and are described more completely in a published manuscript (Nucleic Acids Research 2007; doi: 10.1093/nar/gkm918).
These scripts have been designed to work in our processing environment. The download package includes README files, as well as comments in the individual scripts that should help you adapt them to your environment. However the task of adapting these scripts may not be trivial. We offer these scripts "as-is" in the hopes that they will be useful to some in the research community.
These scripts require the MUMmer sequence alignment tools, which are available for download here. They also make use of the binding energy calculator from the ArrayOligoSelector package (Bozdech et al, http://genomebiology.com/2003/4/2/R9). The source code for the energy calculator is included with our scripts.
Click here to download the scripts as a compressed tar archive.