Oligonucleotide design software tools | Microarray data analysis

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.

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.

Allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize.

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.

Integrates a probe quality score calculation. Teolenn is a flexible and universal probe design solution based on an open module system approach. It works as a four-step workflow and it probes: (i) library creation, (ii) parameter calculation, (iii) filtering and (iv) selection. It also assigns a quality score to each designed probe so that a posteriori filtering steps and correlations can be made.