FASTPCR

FASTPCR performs PCR primer and probe design and oligonucleotide analyses for diverse PCR, genotyping, assembly, and targeted sequencing applications.

Key Features:

• Primer and probe design for multiple PCR types: Designs primers and probes for standard PCR, multiplex PCR, long-distance PCR, inverse PCR, real-time PCR with TaqMan probes, Xtreme Chain Reaction (XCR), group-specific PCR, and overlap extension PCR for multifragment assembly cloning.
• Isothermal amplification support: Designs oligonucleotides for isothermal amplification methods including Loop-mediated Isothermal Amplification (LAMP).
• Long-sequence assembly oligonucleotides: Designs specific oligonucleotide sets for long sequence assembly using ligase chain reaction.
• Multiplex amplicon tiling: Supports multiplexed designs of overlapping and nonoverlapping DNA amplicons that can tile across target regions for targeted next-generation sequencing.
• KASP genotyping assay design: Facilitates competitive allele-specific PCR (KASP)-based genotyping assay design for detection of single-nucleotide polymorphisms and insertions/deletions.
• In silico PCR and primer analyses: Performs in silico PCR primer and probe searches with detailed analyses of individual primers and primer pairs.
• Sequence analysis suite: Provides sequence analysis functions including pattern searching and sequence similarity and conservancy analysis.
• Restriction enzyme analysis: Performs restriction enzyme analysis for I-, II- and III-type endonucleases.
• Contig assembly and consensus: Supports assembly of contiguous sequences and generation of consensus sequences.
• Repeat detection and visualization: Detects and visually displays various repeat types within sequences to aid identification of structural genomic elements.
• Batch processing: Enables batch processing of sequence files for high-throughput analyses.

Scientific Applications:

• PCR assay development: Design and validation of primers and probes for standard, multiplex, long-distance, inverse, and real-time PCR assays including TaqMan assays.
• Isothermal assay development: Design of oligonucleotides for LAMP and other isothermal amplification assays.
• Targeted NGS amplicon design: Creation of overlapping and nonoverlapping amplicon panels for targeted next-generation sequencing and tiling across genomic regions.
• Genotyping of variants: Design of KASP assays for SNP and indel genotyping at specific loci.
• Long-sequence assembly: Design of oligonucleotides for ligase chain reaction-based long-sequence assembly.
• Cloning and construct assembly: Primer design for overlap extension PCR and multifragment assembly cloning workflows.
• Restriction mapping and pattern analysis: Restriction enzyme site analysis and pattern searching for cloning and molecular biology planning.
• Repeat and structural element analysis: Detection and analysis of sequence repeats and structural genomic elements.

Methodology:

Computational methods explicitly include in silico PCR primer/probe search and detailed primer/pair analyses, sequence analysis, I-II-III-type restriction enzyme analysis, pattern searching, contiguous sequence assembly, consensus sequence generation, sequence similarity and conservancy analysis, repeat detection and visualization, and batch processing of sequence files.