Bioinformatics tools for PCR

PCR primer design

Primer3Plus: Picks primers from a DNA sequence

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PCR primer design

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

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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

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PCR primer design

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

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PCR primer design

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

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PCR primer design

Oligo Calc: Oligonucleotide Properties Calculator

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Database

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

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Database

ViPR: Virus Pathogen Database and Analysis Resource

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Database

Monocots PLAZA 4.5 : comparative genomics in plants for monocots

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Bioinformatics tools for NGS

Denovo assembly

Trinity: RNA-Seq De novo Assembly Using Trinity

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Denovo assembly

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

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Denovo assembly

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

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RNAseq read QC

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

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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.

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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.

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Gene analysis

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

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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.

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Gene analysis

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

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