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AMPLIFX SOFTWARE

Two independent text editors at different TAB: Sequences, Pre-designed primers (probes) list. Efficient and complete detection of different types of repeats and any type of tandem repeats, from short tandem repeats (microsatellites) to large satellite sequences with a summary table of the types and locations of the found repeats.Ĭomparison of primer design and oligonucleotide analysing tools versus other most popular on-line primer design and analysing packages.the program includes various bioinformatics tools for patterns analysis of sequences with GC:(G-C)/(G+C), AT:(A-T)/(A+T), SW:(S-W)/(S+W), MK:(M-K)/(M+K), purine-pyrimidine (R-Y)/(R+Y) skews, CG% and GA% content and the melting temperature and considers linguistic sequence complexity profiles.Polymerase Chain Assembly (PCA) - created to automate the design oligonucleotide sets for long sequence assembly by PCR.translates nucleotide (DNA/RNA) sequences to the corresponding peptide sequence in all six frames for standard and degenerate DNA and modifications (inosine, uridine).tool for searching for similar sequences (or primers).tool for restriction I-II-III types enzymes analysis, find or create restriction enzyme recognition sites for coding sequences.tool for identifying simple sequence repeat (SSR) loci by analysing the low complexity regions of input sequences.tool calculate Tm for primer dimers with mismatches for pure and mixed bases using averaged nearest neighbour thermodynamic parameters and for modifications (inosine, uridine, or LNA).

primers (probes) are analyzed for all primer secondary structures including the alternative hydrogen bonding to Watson-Crick base pairing such as G-quadruplexes or wobble base pairs (like G-G, G-T, G-A), self-dimers and cross-dimers in primer pairs.

analyzes different features of multiple primers simultaneously, the melting temperature, GC content, sequence linguistic complexity, primer PCR efficiency and molecular weight, the extinction coefficient, the optical density (OD).

comprehensive primer test, the melting temperature calculation for standard and degenerate oligonucleotides including LNA and other modifications, primer's PCR efficiency and linguistic complexity, and dilution and resuspension calculator.

in silico (virtual) PCR for primers and probes searching or in silico PCR against genome(s) (or a list of chromosome) - prediction of probable PCR products and search of potential mismatching location of the specified primers or probes.

AMPLIFX SOFTWARE

java application is based on FastPCR software for Windows and provides comprehensive and professional facilities for designing primers for most PCR applications and their combinations: standard, multiplex, long distance, inverse, real-time, Xtreme Chain Reaction (XCR®), group-specific (universal primers for phylogenetically related DNA sequences) or unique (specific primers for each from phylogenetically related DNA sequences), bisulphite modification assays, polymerase extension PCR multi-fragments assembly cloning (OE-PCR), Loop-mediated Isothermal Amplification (LAMP) microarray design Allele-Specific PCR (AS-PCR) - KASP™ (Kompetitive Allele Specific PCR) or PACE™ (PCR Allele Competitive Extension) based genotyping assay design for biallelic discrimination of single nucleotide polymorphisms (SNPs) and insertions and deletions (Indels) at specific loci.