These are the official documentation files for BioSap software.In here you will find usage instructions, technical caveats,
important limitations to be aware of, error message decodings,algorithm explanation, development information, and potentially more.
The advent of custom designed oligonucleotide microarrays made possible by recent advancements in ink-jet microarray synthesis technology, provides the opportunity to quickly iterate through different microarray experiments. This necessitates designing oligonucleotides quickly, effectively, and by using previously gathered information for more optimal design. The BIOSAP project provides the opportunity to design thousands of oligonucleotides to a given set of biological DNA sequences. The features (oligos) reported are guaranteed to be unique among all features chosen, have certain properties based on the requirements specified by the user, are checked for potential self-hybridizing properties, and are BLAST (Altschul et al., 1990) searched for possible close alignments to genomic sequences other than one for which the given feature was chosen. The final output of BIOSAP is an XML document containing the details and results of the search. This data can be imported into a database to be searched for future iterations of microarray design.