Oligonucleotide design software tools | Microarray data analysis
DNA microarrays have become ubiquitous in biological and medical research. The most difficult problem that needs to be solved is the design of DNA oligonucleotides that (i) are highly specific, that is, bind only to the intended target, (ii) cover the highest possible number of genes, that is, all genes that allow such unique regions, and (iii) are computed fast.
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.
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.
Assists users in the design of microarray probe sets. YODA can design one or multiple oligo probes per sequence with the possibility to customize the parameters such as, among others, oligo length, maximum percent identity with a non-target sequence or melting temperature range. This software supports three classes of DNA sequence files (design, genome and host) to achieve multiple design strategies.