PrimerDigital

References apply to all FastPCR update, if you use FastPCR in your work please cite:

Kalendar R, Khassenov B, Ramankulov Y, Samuilova O, Ivanov KI 2017. FastPCR: an in silico tool for fast primer and probe design and advanced sequence analysis. Genomics, 109(4-5): 312-319. DOI:10.1016/j.ygeno.2017.05.005

Kalendar R, Tselykh T, Khassenov B, Ramanculov EM 2017. Introduction on using the FastPCR software and the related Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Methods in Molecular Biology, 1620: 33-64. DOI:10.1007/978-1-4939-7060-5_2

Kalendar R, Muterko A, Shamekova M, Zhambakin K 2017. In silico PCR tools a fast primer, probe and advanced searching. Methods in Molecular Biology, 1620: 1-31. DOI:10.1007/978-1-4939-7060-5_1

The licenses are available for all, commercial or non-commercial users who wish to use the PrimerDigital software products. If you want to purchase our program and further information regarding FastPCR licensing, please contact PrimerDigital by e-mail.

• Multiple changes in program code;
• New feature: in silico probe search in "in silico PCR" tool (also searching for degenerated primer(s) or probe(s));
• New feature: calculation temperature melting (Tm) for primer-dimer and in silico PCR with mismatches;
• New feature: the temperature melting calculation for normal and degenerated nucleotide combinations based on the nearest neighbor thermodynamic parameters is included;
• Primer dimer detection algorithm is changed;
• New feature: multiplex PCR primers design;
• New feature: search for LTR-retrotransposons;
• New feature: search for similar primers;
• New feature: instant alignment algorithm search developed;
• New feature: data format showing and task identification;
• New feature: PCR primer and probe design much improved;
• Added Open Long Sequence(s) (chromosome);
• Added new data reading formats - TAB column and Excel sheet;
• Added new data reading formats - alignment, MSF, MEGA;
• Added Unique PCR primers design;
• Added Multitasking PCR primers and probes design;
• Added Tool - Linguistic sequence complexity.
• Added Tool - Generated Random DNA Sequence.
• Added Tool - Consensus Sequence;
• Added Tool - Pair Sequences Similarity;
• Added Tool - GA% plot;
• Added Tool - Purine-Pyrimidine plot;
• Fixed bug with PCR primer design;
• Fixed bug with in silico PCR;
• Fixed bug with alignment algorithm;
• Several non-critical and two critical errors are fixed in PCR primer design;
• EMBL format is accepted;
• Add control for global PCR primers design parameters;
• Improves algorithm for primers (probes) screening through reference sequence (the secondary (non-specific) binding test);
• Add the LUX (self-quenched) primers design for quantitative PCR;
• Alignment format is accepted;
• Improving of the SSR screening algorithm;
• Add of direct SSR PCR primers design;
• Large improving of the probes design algorithm;
• Add of tools for MITE elements and SSRs searching;
• Probes design algorithm is improved;
• Tool for MITE retroelements searching add;
• Tools added: "Reverse In silico PCR" for detection inverted repeats, potential single-priming PCR;
• Consensus sequence tool add;
• Alignment algorithm updated;
• Multiplex PCR report update;
• Tm calculation added simple formulas;
• "in silico" PCR add PCR size prediction for circular sequence;
• "Molecular Beacon Design" tools is update;
• PCR primer design for related sequences (group specific PCR);
• "Molecular Beacon Design" tools is update;
• Protein-protein alignment with BLOSUM62 amino acid substitution matrix (beta algorithm);
• Add option for overlapping primers control (-op=true or false);
• File with MEGA format, GenBank format and Blast Queue WEB alignments result is accepted;
• For "Molecular Beacon Design" tools add multilocus cross homologies test;
• "Molecular Beacon Design" and "Native Molecular Beacons" tools is update (add pre-designed primer list). Checks molecular beacons for cross homologies with all primers preventing competition in multiplex reactions;
• Add new "Molecular Beacon Design" tool and command -mbN1-N2 for localization target molecular beacon site;
• Add to "Molecular Beacon Design" - tool for searching the native molecular becons in sequence;
• Multiplex PCR report include the length of PCR products and PCR product size control added;
• XML report of PCR primers design;
• Advanced simple repeats search it is added in software (it can find any simple repeats with any nucleotides compositions). The algorithm based on search the low-complexity  regions;
• Add command for PCR primer design "-pr=true|false" for reporting primers in result file;
• "/?" add for loading PCR primers design options;
• Multiplex PCR report is improved (show compatibility of pair primers combination);
• Add "Report Group-Specific Combination of Pair Primers", for similar sequences;
• Add degenerated nucleotides for powerful search;
• Commands in PCR primers design (see more manual or in program "PCR Help");
• The program accepts the universal degenerate DNA code for definition of the 3'-end of primers;
• Add "Restriction Analysis" (it will be improved, soon) (enzymes from "BioLabs" and "Fermentas");
• The formula for calculation "optimal annealing Tm of PCR" is changed and became higher at 7.4 degrees that corresponds to supervision at the analysis in gradient PCR;
• The program supports a new format for PCR primer design, containing area for primer design for left primers and right primers both given minimal and maximal size PCR product in brackets "( )" simultaneously. Size PCR product it is possible to have in any place after ">" and a name sequence;
• The data are showing in "Microsoft Excel" sheet;
• "In silico PCR" add into the program;
• Primer duplication control algorithm is improved;