Using Array Designer, you can design probes for thousands of sequences in a single search run. Complete user control is available to alter the design parameters to meet specific research needs. You can batch BLAST sequences and avoid repeats and low complexity regions before designing probes.
Automatic Homology Avoidance: BLAST searches hundreds of sequences in a single search run. The results are automatically interpreted and the homologies identified are avoided during probe design.
Specificity Check: BLAST searches the primers and probes designed against all the genomic databases available at NCBI, including the redundant nr database, to verify the specificity of design.
Product Location: Allows specifying the product length and product location viz at the 3’end, 5’end or anywhere in the sequence.
Comprehensive Selection Criteria: Screens oligos for their thermodynamic properties as well as secondary structures. Graphics for the structures are also displayed.
Ranking: Uses statistical optimization techniques to design the best primer and probe for each template. A list of alternate designs is also available.
Algorithm: Calculates oligo Tm using nearest neighbor thermodynamic algorithm.
Array Designer designs thousands of primers and probes for oligo and cDNA microarrays in seconds. It designs probes for SNP detection, microarray gene expression and gene expression profiling. In addition, comprehensive support for tiling arrays and resequencing arrays is available.
Array Designer designs highly specific oligos by interpreting the results of a BLAST search performed against any genomic database available at NCBI or a local custom database. Any significant homologies identified are automatically avoided while designing oligos. Repeat regions are identified and automatically avoided.