Bioinformatics Software Development Projects

FPGA Assisted Equine Gene Annotation and Custom Microarray (Genechip®)

Principal Investigator: Alicia Bertone, Ohio State Unviersity
Funding agency: Ohio State University
Duration: 5/2002 - 4/2004

DNA microarrays are small, solid supports containing thousands of gene sequences that are immobilized or attached at fixed locations. This technologic advance has revolutionized the basic approach to research as hundreds to thousands of genes can be analyzed simultaneously under identical conditions to assess various biological models, including disease, therapy, or experimental manipulation. Mammalian commercial microarrays currently exist for human, mouse, and rat, but not for the horse.

Sequence selection and probe design are crucial for the reliability, sensitivity, and specificity of DNA microarrays. The completed human genome consists of ~3,000 mega-bases and ~ 35,000 genes distributed across 23 chromosomes. The mouse genome is in similar size and gene number, except with 3 fewer chromosomes. These genetic data are good templates in comparative analysis to annotate gene information of other organisms. However, huge computation is involved in sequence similarity comparisons. Currently, a public nucleotide sequence database maintained at the National Center for Biotechnology Information (NCBI) contains > 20,000 equine related sequences, which are sufficient for the generation of the first equine DNA microarray. Several challenges exist for the equine DNA microarray design:

1). There is no public algorithm and software available for DNA microarray design;
2). Not all available equine sequence data are suitable for DNA microarray;
3) There is significant data redundancy and replication in the equine public database. Hence, the data need to be pruned;
4). Significant equine gene data with unknown function need to be annotated by comparative analysis against the annotated human and mouse data.

Field Programmable Gate Arrays (FPGA) are integrated circuits designed to perform particular types of calculations far more quickly than conventional, general-purpose CPUs. In this sense, FPGAs are similar to the application-specific integrated circuits (ASICs) used for a variety of single-purpose processing tasks. However, unlike with ASICs, programmers can use software to "rewire" FPGA circuits for different processes of calculations. TimeLogic has developed DeCypher system based on the FPGA technology with accelerated biocomputing algorithms, including BLAST for genome-level analysis.

Here, we describe a unique DNA microarray design algorithm using the FPGA technology combined with de novo software development.

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