Oligonucleotide design software tools | Microarray data analysis

A Java software project aimed at providing a framework for design and analysis of sets of oligonucleotide probes for use in multiplex assays for nucleic acid analyses and other purposes.

Permits users to design hundreds of specific oligos for single-nucleotide polymorphism (SNP) detection or expression studies or hundreds of polymerase chain reaction (PCR) primer pairs for cDNA microarrays. Array Designer assists users in studying entire organisms 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)

A powerful tool for microarray probe design that allows for integration of sequence annotation, such as exon/intron structure, untranslated regions (UTRs), transcription start site, etc. In addition to probe selection according to a series of probe quality parameters, cross-hybridization, T(m), position in transcript, probe folding and low-complexity, the program facilitates automatic placement of probes relative to the sequence annotation. The program also supports automatic placement of multiple probes per transcript. Together these facilities make advanced probe design feasible for scientists inexperienced in computerized information management.

Models open reading frame (ORF)-specific DNA microarrays. ArrayOligoSelector allows the selection of unique sequences from predicted ORFs of any genome. This program considers every ORF and optimizes the oligonucleotide selection according multiple parameters such as sequence complexity or GC content. Lastly, it ranks candidates oligos by distance from 3’ end. Users are also allowed to define customized patterns for filtering.

Designs specific oligonucleotides at the genomic scale. OligoArray computes gene-specific and secondary structure-free oligonucleotides for genome-scale oligonucleotide microarray construction. This program also uses the Lempel-Ziv (LZ) sequence complexity criteria, and allows the design of oligonucleotides for use on microarrays for gene expression profiling. It can manage neither polymorphism nor splicing variants, except by considering each variant as a different input sequence.