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    Bioinformatics Tool

    HOME  >  R&D  >  Bioinformatics Tool

    Bioinformatics tools for PCR

    Purpose

    Description

    Link

    PCR primer design

    Primer3Plus: Picks primers from a DNA sequence

     

    PCR primer design

    Primer-Blast: Tool for finding primers specific to PCR template

     

    PCR primer design

    OligoArchitect™: can get to work designing one of five different types of probe: SYBR Green I, Dual-Labeled, Molecular Beacon, Scorpions, or LightCycler probes

     

    PCR primer design

    OligoEvaluator™: The most powerful and comprehensive package to analyze DNA oligo to successful PCR

     

    PCR primer design

    Multiple Primer Analyzer: For analyzing and comparing multiple primer sequences simultaneously such as self and cross dimer analysis and TM calculate

     

    PCR primer design

    Oligo Calc: Oligonucleotide Properties Calculator

     

    Database

    GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences

     

    Database

    ViPR: Virus Pathogen Database and Analysis Resource

     

    Database

    Monocots PLAZA 4.5 : comparative genomics in plants for monocots

     

    Bioinformatics tools for NGS

    Purpose

    Description

    Link

    Denovo assembly

    Trinity: RNA-Seq De novo Assembly Using Trinity

     

    Denovo assembly

    IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads

     

    Denovo assembly

    ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes.

     

    RNAseq read QC

    AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

     

    RNAseq read QC

    FastP: A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.

     

    RNAseq read QC

    Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.

     

    Gene analysis

    TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity.

     

    Gene analysis

    BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

     

    Gene analysis

    CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

     

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