Invirustech-Eng

Bioinfomatics tools for PCR

Purpose

Description

Link

PCR primer design

Primer3Plus: Picks primers from a DNA sequence

https://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi

PCR primer design

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

https://www.ncbi.nlm.nih.gov/tools/primer-blast/

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

http://www.oligoarchitect.com/

PCR primer design

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

http://www.oligoevaluator.com/

PCR primer design

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

https://www.thermofisher.com/kr/ko/home/brands/thermo-scientific/molecular-biology/molecular-biology-learning-center/molecular-biology-resource-library/thermo-scientific-web-tools/multiple-primer-analyzer.html

PCR primer design

Oligo Calc: Oligonucleotide Properties Calculator

http://biotools.nubic.northwestern.edu/OligoCalc.html

Database

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

https://www.ncbi.nlm.nih.gov/genbank/

Database

ViPR: Virus Pathogen Database and Analysis Resource

https://www.viprbrc.org/brc/home.spg?decorator=vipr

Database

Monocots PLAZA 4.5 : comparative genomics in plants for monocots

https://bioinformatics.psb.ugent.be/plaza/versions/plaza_v4_5_monocots/

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Bioinfomatics tools for NGS

Purpose

Description

Link

Denovo assembly

Trinity: RNA-Seq De novo Assembly Using Trinity.

https://github.com/trinityrnaseq/trinityrnaseq/wiki

Denovo assembly

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

https://github.com/loneknightpy/idba

Denovo assembly

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

https://github.com/bcgsc/abyss

RNAseq read QC

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

https://github.com/OpenGene/AfterQC

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.

https://github.com/OpenGene/fastp

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.

https://github.com/usadellab/Trimmomatic

Gene analysis

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

https://github.com/TransDecoder/TransDecoder/wiki

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.

https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

Gene analysis

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

http://weizhong-lab.ucsd.edu/cd-hit/

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INVIRUSTECH

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R&D center : (61222) 4F, 100, Seoam-daero, Buk-gu, Gwangju, S.Korea

CEO : Park, Kibeom E-mail : invirustech@invirustech.com TEL : +82-62-511-0682 FAX : +82-62-531-0682

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