Microarray Gene Expression

Probe and Primer Design

Choices in Probe Design: Array Designer can design single or multiple probes per sequence for your microarray projects. Allows specifying the minimum distance between two probes to avoid overlapping.

Product Location: Allows specifying the product (amplicon) 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.

Specificity Check: Thousands of searches are submitted automatically. Results are interpreted and displayed in the Homology Avoidance window.

Batch Sequence BLAST Search: Array Designer can BLAST search hundreds of sequences. The results are interpreted and the homologies identified are avoided while designing primers.

Local BLAST: Array Designer can BLAST search against a custom local database that can be set up on a Unix machine using the WWW Standalone BLAST facility of the NCBI. Read the inbuilt product help for details.

Desktop BLAST: BLAST search sequences against local custom databases without the need of setting up a server on a separate machine. Simply save the sequence files (.txt or .fa) on your computer and ask Array Designer to BLAST search your query sequence against them.

Verification of Specific Design: The primers and probes designed by the program can be BLAST searched against all the nucleotide databases available at NCBI to verify the specificity of design.

Repeat Regions: Optimizes BLAST search parameters to detect human repeats while searching the human RNA (previously called mRNA) database at NCBI.

SNP Loading: Easily add a single SNP at a time or load thousands of SNPs using standard GenBank variation files.

SNP Detection: Designs probes for SNP detection (both wild and mutant) with SNP at the center of the probe.

SNP Genotyping with Array Designer: Designs SNP genotyping probes with SNP or one base upstream of the 3' end of the probe.

By Length: Probes can be designed for the fragments of a size chosen by the user. The sequence is broken down into small equal-sized fragments and then a specific probe is designed for each one of them.

By Position: Probes can be designed on genes/fragments, the start and stop position for which can be imported from a text file.

By Annotation: Probes can be designed on genes or exons, the annotations for which can be read from the GenBank file.

BLAST to Ensure Specificity: 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.
Sequence Size: Array Designer can design probes spanning the entire genome of the organism. This ability is especially useful to study the expression of intergenic and intragenic regions. Fragments to be studied can be generated on the basis of their length, their position or by specifying an annotation such as gene, exon or both.
Uniform Tm Values: Array Designer designs probes free of secondary structures and with uniform Tm values ensuring a high rate of success of microarray experiments.

Sequence Size: Array Designer can design tiling primers to study protein binding regions of small to medium sized genomes. You can generate both distinct or overlapping amplicons depending on the specificity desired.

Distinct Amplicon: Primers are designed such that there is no overlap between adjacent amplicons.

Overlapping Amplicon: Primers are designed such that the adjacent amplicons overlap each other in the flanking regions.

Resequencing Probe Design: In addition to standard probes, Array Designer also designs resequencing arrays. With custom resequencing arrays, you can detect SNP and other sequence variations in a large number of samples for applications such as biowarfare pathogen studies, bacterial identification, predisposition and resistance to disease or discovering the genetic basis of phenotypic traits.

BLAST Search: The challenge in designing chips for resequencing by hybridization is to achieve the lowest possible false positive rate. Array Designer offers an innovative and unique project BLAST capability to identify these regions and recommends a multi-chip solution.

Avoiding Repetitive Regions: You can simply connect to the popular Repeat Masker using the handy link and Array Designer will avoid creating spots that may generate false positives.