CRISPR tools

Defense system finder

Tool to predict Bacteriophage defense systems

 

CRISPRCasTyper

Tool to predict CRISPR-Cas type and much more

 

CRISPR-Cas finder ++

Tool to find CRISPR arrays and Cas genes

 

CRISPRfinder

Tool to find CRISPR arrays and select spacers

 

CRISPRdb

Database of CRISPR arrays

 

CRISPRtarget

Tool to predict targets of CRISPR spacers

 

CRISPRdetect

Tool to predict CRISPR arrays and Cas gene systems

 

CRISPRmap

Tool to analyze CRISPR repeat structure

 

CRISPi

Interactive CRISPR suite

 

Chop Chop

Tool for Cas9 and Cpf1 target selection

 

Genome editing tools (Cas9 / Cas12a)

Various links to genome editing tools

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Other tools

AlphaFold2

 

FLAGS

 

Jalview

 

Blast at NCBI

 

BlastP in Paris

 

IMG - Integrated microbial genome database

 

STRING - Protein networks and genomic neighbourhood

 

Interpro

 

Pfam

 

SMART - Protein domain prediction

 

Protein calculator - Prediction tool for protein properties (mass etc.)

 

Phyre 2 – Protein structure prediction

 

iTasser – Protein structure prediction

 

iVirus - Virus bioinformatics suite

 

PDB database - Protein structure

 

EM structure database

 

Signal P - Signal peptides  in proteins

 

Weblogo - Motif finding and representation

 

Phaster - Prophage prediction

 

Phast - Prophage prediction

 

Phagonaute – Phage gene ontology

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Server

• ClustalW2 :multiple sequence alignment program

• BLAST: Basic Local Alignment Search Tool

• DALI: Comparing protein structures in 3D

• SCOP: Structural Classification of Proteins

• CATH: Classification of protein domain structures

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Data bank

• PubMed

• Expasy

• PDB (Protein Data Bank)

• NBD (Nucleic Acid Database)

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Journal

• Nature

• Cell

• Science

• NSMB

• PNAS

• RNA

• PLoS

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Data processing

• CryoSPARC

• Relion

• HKL

• MOSFLM

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Structure determination

• CCP4 suite

• CNS

• SOLVE/RESOLVE

• SHELX

• ARP/wARP

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Molecular graphics

• O

• COOT

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Molecular viewer

• PyMOL

• CCP4mg