Array Designer project can help design thousands of efficient, highly specific oligos to make microarrays for SNP genotyping and expression studies with the click of a button.
For investigating gene control elements in the post-sequencing era, the software designs tiling arrays for interrogating intragenic and intergenic regions and now the software also designs resequencing arrays for analysis of large genomic sequences and genetic variation within the clinical trial population.
Here are some key features of "Array Designer":
· Oligo microarray software: Array Designer designs highly specific oligo microarray for SNP genotyping and expression studies.
· Oligo microarray design software which helps you design probes for expression and SNP studies.
· Array Designer is a highly flexible and scalable microarray software, for designing oligos/primers for large projects.
· Array Designer is a microarray software which offers a high-throughput, greatly automated approach for designing highly specific optimal oligonucleotide probes for microarray experiments.
· cDNA microarray design: Array Designer by default, uses optimized design parameters for cDNA microarray design.
· For DNA microarray design, the carefully chosen default parameters help make the design a success.
· Array Designer, with its highly sophisticated algorithm, may be the best available dna microarray software for microarray design.
· Whole genome array-Whole genome arrays have been useful for studying the poorly understood aspects of trancriptome, natural antisense transcript because they can simultaneously monitor gene expression on both strands of genome
· Tiling array- Tiling array are used to investigate transcription factor binding sites TFBS, not only upstream of genes but also in intronic and intergenic regions.
· Resequencing arrays- In addition to standard probes, Array Designer also designs resequencing arrays useful for analysis of large genomic sequences and genetic variation within the clinical trial population.
· Flexible input formats- Supports sequences in GenBank, FASTA. Loads multiple sequences from a single GenBank or FASTA format file.
· Standard PCR Reaction Conditions- Optimizes PCR primers on all sequences to amplify with uniform reaction conditions.
· Multiple probes- Designs the best probe per sequence or multiple probes per sequence for increased accuracy of detection.
· SNP detection- Designs SNP probes for both hybridization and primer extension detection.
· Flexible Hybridization Probe Locations- Probes can be designed to span each site, or can have 3' end anchored at each site, or can be optimized within a specified region around the site.