Designs oligonucleotide baits for hybrid selection reactions. This tool is used to design custom bait sets for hybrid selection experiments. The following files are input into BaitDesigner: a (TARGET) interval list indicating the sequences of interest, e.g. exons with their respective coordinates, a reference sequence, and a unique identifier string (DESIGN_NAME). The tool will output interval_list files of both bait and target sequences as well as the actual bait sequences in FastA format. At least two baits are output for each target sequence, with greater numbers for larger intervals. Although the default values for both bait size (120 bases) nd offsets (80 bases) are suitable for most applications, these values can be customized. Offsets represent the distance between sequential baits on a contiguous stretch of target DNA sequence. The tool will also output a pooled set of 55,000 (default) oligonucleotides representing all of the baits redundantly. This redundancy achieves a uniform concentration of oligonucleotides for synthesis by a vendor as well as equal numbersof each bait to prevent bias during the hybrid selection reaction.
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