Oligonucleotides

Primrose is a simple, Java based application designed to help you identify potentially useful oligonucleotides for use as probes or PCR primers as phylogenetic tools. Platforms: Windows

TmCheck is a simple, Java based application specially designed to help you calculate the melting temperature of oligonucleotides. Able to calculate Tm according to the Wallace rule, the Marmur-Schildkraut-Doty equation, the Chester and Marshak equation, and the Nearest Neighbour method. Platforms: Windows

OligoLocator is a simple, Java based application designed to identify the position of oligonucleotides within nucleic acid sequences with varying degrees of mismatch between the two. Platforms: Windows

OligoCounter is a Java command line program which counts overrepresented 8-14bp oligonucleotides in DNA sequences. These oligos can be useful in visualising small genomes on a global basis (see figure below), investigating repeats at certain regions, and for attributing short reads (for example... Platforms: Mac

Nowadays, the use of so-called RNA interference is a common technique applied by molecular biologists to determine the function of the many genes in our genome.Unfortunately, the design of oligonucleotides, the building blocks for this technique, is a time-consuming and error-prone task. iRNAi... Platforms: Mac

OLIGO is a multi-functional program that searches for and selects oligonucleotides from a sequence file for polymerase chain reaction (PCR), DNA sequencing, site-directed mutagenesis, and various hybridization applications. It calculates hybridization temperature and secondary structure of... Platforms: Mac

FONZIE is a bioinformatic tool written in Python developed for the genetic cartography speciality. FONZIE allow as well to find markers on a set of sequences than to find associate oligonucleotides. http://www.biomedcentral.com/1756-0500/3/322/abstra Features . Requirements: Python, Tandem... Platforms: *nix

provides comprehensive analysis of sequence with standard and mixed bases, as well as DNA, RNA, methylated, locked and phosphorothioated bases; tool will calculate the physical properties of the sequence including length, CG content, melting temperature, molecular weight, the extiction... Platforms: Mac

analyzes different features of multiple primers simultaneously, the melting temperature calculation for standard and degenerate oligonucleotides, GC content, primer PCR efficiency; primers are analyzed for all primer secondary structures including G-quadruplexes detection, hairpins, self-dimers... Platforms: Mac