The Computational/Bioinformatics Core will be integral to all four of the projects in the Program Project but will be of particular importance to Projects 1 and 2. For Project 1, tools for assembly of contigs, identification and automated and manual annotation of genes, and databases for the storage of assemblies, genes, annotations, sequences, primers for cloning and for tracking of the cloning process are all already in place. Most applications make use of existing tools (BLAST, CAP3, Apollo viewer, Gbrowse) linked with Perl scripts to automate the processes. Future efforts will include integrating the fully assembled and annotated T. cruzi genome into the workflow. In addition, tools will be added to track the results of vaccination trials on a gene-by-gene basis. Project 2 uses commercial software (Matrix Mascot) for matching mass spectra to our ORF databases but requires significant scripting for the automation of pre- and post-Mascot analysis. In addition, tools to extract the maximum amount of information from the ms/ms data are in development, including de novo sequencing tools. The results of vaccine trials in Project 3 will be added to our database of genes as each gene is examined individually or in pools and a patient database will be used to track the results from Project 4. Maintenance of this infrastructure and the addition of new tools will be the job of this core.
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