Scans automatically target DNA sequences and designs primers in regions of low degeneracy that are free of secondary structures (hairpins, dimers and false priming sites). Primer Premier searches for optimal polymerase chain reaction (PCR), multiplex and single nucleotide polymorphism (SNP) genotyping primers via a nearest neighbor algorithm. It supports multiplex assays and can automatically describe BLAST search results.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Allows DNA, RNA, and protein sequence data analysis. CLC Main Workbench is a comprehensive workbench. A primer design functionality offers graphical interaction during the primer selection process. The software also allows to show the annotations of the individual sequences in a multiple sequence alignment, offers graphically advanced in silico cloning and design of vectors, BLAST searches on protein and DNA sequences, and other feature such as Assembly, Phylogeny, Workflow, Molecular structure visualization and development of plug-ins.
Helps users design target-specific primers. Primer-BLAST is a web application that offers flexibility to accommodate different primer design. It incorporates a global alignment mechanism and is designed to be very sensitive in detecting potential amplification targets. Users can either design new primers or check the specificity of pre-existing primers. Finally, it has the capability to place primers based on exon/intron boundaries and Single-Nucleotide Polymorphism (SNP) locations.
Provides extensive live design customization and can be used to design assays for species other than human, mouse, and rat. PrimerQuest design tool that enables customers to design primers and probes for a wide variety of applications. The advantage of using the PrimerQuest program lies in its customizable designs, which allows users to adjust reaction conditions (e.g., primer, salt, and Mg2+ concentrations), force use of a particular primer or probe sequence, and specify design regions.