Array Designer 4

Introduction

Premior Biosoft's Array Designer 4 is a comprehensive desktop tool to efficiently design hundreds of specific oligos for SNP detection or expression studies or hundreds of PCR primer pairs for cDNA microarrays. You can efficiently retrieve, analyze and store data.

Arrays for the post-sequencing Era

• Whole Genome Arrays: With Array Designer you can study entire organisms effortlessly by detecting every gene or exon in the whole genome, characterizing transcriptomes, discovering differentially and alternatively spliced transcripts, SNP discovery and genotyping, DNA sequence variation in individuals or populations and comparative genome hybridization (CGH)
• Tiling Arrays: You can even design tiling arrays to spot every base of a long genomic sequence, avoiding repetitive regions. Designing arrays to characterize regulatory elements, or to study epigenetic modifications, methylation patterns and protein binding sites has never been so easy.
• Resequencing Arrays: Array Designer designs resequencing arrays with which you can detect SNP and other sequence variations in a large number of samples for applications such as biowarfare pathogen studies, predisposition and resistance to disease or discovering the genetic basis of phenotypic traits. With a unique feature which we call "Project BLAST", you can identify and avoid the homologous regions that create false positives

Design Highly Specific Oligos

To ensure specific amplification and exact detection, Array Designer designs highly specific PCR primers and oligos by automatically avoiding regions of significant cross homologies identified during a BLAST search against a private local database or the genomic public databases available at NCBI. For a whole genome sequence, Array Designer automatically creates a local custom database of the input sequence and BLAST searches every fragment against it. To verify the specificity of design, you can BLAST the designed oligos.

Beyond NCBI Database Support

When working with confidential or publicly unavailable sequences, you can set up a local database either on a Unix based server for institution-wide access or on a PC for your own convenience.