인바이러스테크

Bioinfomatics tools for PCR

Purpose

Description

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

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