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
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Bioinfomatics tools for NGS
Purpose
Description
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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