BIOSAP Oligonucleotide Reporter Software

Oligonucleotide Prediction Software

BioSap and Featurama are two linked tools that allow researchers to design of custom oligonucleotide arrays to using any gene sequences in FASTA format. The software allows the user to define a number of important variables similar to those commonly used in the design of PCR primers. The primary parameters are the Melting Temperature (T_m), Maximum and Minimum length, and T_m Range. Featurama outputs an XML and text file of non-duplicate features (sub-sequences of the input sequences, each meeting the parameters of the search) and the BioSap daemon automatically executes a BLAST search on the output file, comparing the Featurama designed probes to a file of sequences from a relevant organism. A document type definition for BioSap is available on the sourceforge web site. The BLAST output is piped to an LSAX implementation that will parse information about close matches to genes other than the target gene or its reverse complement. (LSAX is a modification of the SAX java interface to parses XML written by Robert Hubley at the ISB. It has been submitted to the Bio-Java forum). This process allows researchers to eliminate sequences that could cross-hybridize and give ambiguous results. The default formats are FASTA and XML, and include information that can interface with MIAME compliant databases.