Primer Design

Picky

Picky is an oligo microarray design program that identifies probes that are very unique and specific to input sequences. These calculations are based on parameters inputted by the user including optimal probe length, ideal percentage of guanine and cytosine content, target-melting temperature, salt concentration and the maximum length to which a target sequence matches any non-target sequence.

Reference: H.-H. Chou et al. (2004) Bioinformatics 20: 2893-2902. Download genome *.ffn files from GenBank for use with this program. N.B. Unfortunately these files do not include the gene names only their coordinates.

AiO

AiO (All in One) is a program for Windows, that combines typical DNA/protein features such as plasmid map drawing, finding of ORFs, translate, backtranslate, primer design and virtual cloning. AiO uses databases that allow the management of oligonucleotides, oligonucleotide-manufacturers, restriction enzymes, structural DNA and program users in a multi-user/multi-group environment.

Reference: Karreman C. (2002) Bioinformatics. 18:884-885.

AnnHyb

AnnHyb This programs features include sequence editing with proofreading, format conversion, translation, sequence statistics, probe design & analysis.

MeltCalc

MeltCalc is the ultimate thermodynamic modelling spreadsheet for Excel™ which allows you to analyze probes. See: Spreadsheet software for thermodynamic melting point prediction of oligonucleotide hybridization with and without mismatches.

Reference: Schütz, E., von Ahsen, N. (1999) BioTechniques 27:1218-1224.