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Bioinformatics tools for PCR
PCR primer design
Primer3Plus: Picks primers from a DNA sequence
Primer-Blast: Tool for finding primers specific to PCR template
OligoArchitect™: can get to work designing one of five different types of probe: SYBR Green I, Dual-Labeled, Molecular Beacon, Scorpions, or LightCycler probes
OligoEvaluator™: The most powerful and comprehensive package to analyze DNA oligo to successful PCR
Multiple Primer Analyzer: For analyzing and comparing multiple primer sequences simultaneously such as self and cross dimer analysis and TM calculate
Oligo Calc: Oligonucleotide Properties Calculator
GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences
ViPR: Virus Pathogen Database and Analysis Resource
Monocots PLAZA 4.5 : comparative genomics in plants for monocots
Bioinformatics tools for NGS
Trinity: RNA-Seq De novo Assembly Using Trinity
IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads
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
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.
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.
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity.
BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
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