Degenerate primer design software tools | qPCR analysis
Degenerate primers are a mixture of similar, but not identical primers that are used to amplify a same gene from different organisms. Alternatively, degenerate primers are used when primer design is based on protein sequence, as several different codons can code for one amino acid. Degenerate primers design tools for qPCR are able to calculate and generate primer sequences using specific algorithms.
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.
Designs PCR (Polymerase Chain Reaction) primers from protein multiple-sequence alignments. CODEHOP is suited for cases where the protein sequences are distant from each other and degenerate primers are needed. Isolation of members of a rapidly evolving family of novel cytosine methyltransferase homologs from diverse plants demonstrated his practical utility.
Processes automated computational finishing and annotation of de novo viral assemblies. V-FAT can order and merge contigs, adjust frameshifts and produce NCBI-ready annotation files by using reference and read data. This software performs also several quality assurance measurements like coverage computation by amplicon or gene and identification of potential consensus errors.
Allows to design degenerate primers. GeneFisher2 is a web-based program that helps user to find primers for degenerated sequences. The software incorporates BatCons2 which allows to calculate ambiguous consensus sequence and Back-translation of amino-acid to nucleic-acid-sequences. The software provides four functions: Consensus Backtranslation, Codon Table Backtranslation, DNA and Primer Calculation.
A program for designing pairs of degenerate primers for a given set of DNA sequences. We report on the success of the program in an experimental scheme for identifying all human olfactory receptor (OR) genes. In that project, HYDEN was used to design primers with degeneracies up to 10(10) that amplified with high specificity many novel genes of that family, tripling the number of OR genes known at the time.
Employs suffix array methods for efficient calculations on oligos 10-100 nt in length. PriMux is a software package for selecting multiplex compatible, degenerate primers and probes to detect diverse targets such as viruses. It requires no multiple sequence alignment, instead applying k-mer algorithms, hence it scales well for large target sets and saves user effort from curating sequences into alignable groups.