My Microarray Software Comparison - Probe/Primer Design Software

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Definition of probe/ primer design software
Suggested readings
Probe/ primer design software (in alphabetical order)

[ Array Designer | GAP | OligoArray2 | OligoChecker | OligoPicker | PRIMEGENS | Primer 3 | ProbeWiz Server | ProMide | Sarani | STACKdb | Visual OMP ]

Definition of probe/primer design software

Suggested readings

1. Tomiuk S, Hofmann K. Microarray probe selection strategies. Brief Bioinform. 2001 Dec;2(4):329-40. [PubMed]

Probe/ primer design software (in alphabetical order)

• Array Designer - a software that can design hundreds of primer for DNA or oligonucleotide microarrays, product of Premier Biosoft.
• GAP (Genome- wide Automated Primer finder servers) - design thousands pairs of primers for amplifying a set of open reading frames over an entire genome.
• OligoArray2 - a free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction. Reference [PubMed]
• OligoChecker- A Fully Automatic Solution for Verifying the Specificity of Batch Oligo Designs Against the Whole Transcriptome.
• Oligodb -a web-based system for interactive design of oligo DNA for transcription profiling (hybridization) of human genes. The oligodb system uses the human DNA-transcripts of ENSEMBL. Reference [PubMed][pdf]
• OligoPicker - OligoPicker picks specific oligos by skipping regions with contiguous bases common in other sequences. In addition, oligo specificity is double-checked by NCBI BLAST. Sequence regions similar to non-coding RNAs are avoided because total RNA are often used for array hybridization. Low-complexity regions are also filtered out to maintain oligo specificity. Oligos and sequence regions that may form secondary structures are discarded since both the probes and the sequence target sites should be easily accessible for hybridization. Reference [PubMed]
  
• PRIMEGENS- PRIMEGENS (PRIMEr Design Using GEN Specific Fragments) is a computer program to select gene-specific fragments and then design primer pairs using Primer3 for PCR amplifications. Reference [PubMed]
• Primer3 - a common used software for designing primers for microarray construction.
  
• ProbeWiz Server - The CBS ProbeWiz WWW server predicts optimal PCR primer pairs for generation of probes for cDNA arrays. Reference [PubMed]
• ProMide - ProMide is a collection of command-line tools for Probe selection and Microarray Design.
• Sarani - Sarani Gold (Genome Oligo Designer) is a software for automatic large-scale design of optimal oligonucleotide probes for microarray experiments. Thousands of gene sequences can be analyzed together and best available oligonucleotide probes with uniform thermodynamic properties and minimal similarity to non-specific genes can be selected. Product of Strand Genomics.
  
• STACKdb - The STACKdb, Sequence Tag Alignment and Consensus Knowledgebase, is generated by processing EST and mRNA sequences obtained from Genbank through a pipeline consisting of masking, clustering, alignment and variation analysis steps. The STACKdb database is created using tools called "stackPACK". Also available through Electric Genetics.
• Visual OMP - multiplex primer and probe design optimized to reduce cross-hybridization between oligos and targets, an integrated folding engine for visualizing target and oligo structures, thermodynamics modeling, and built-in BLAST and ClustalW. Product of  DNA Software, Inc.