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Welcome to the CLdb Wiki!

This wiki is a guide to creating a CRISPR loci database and performing workflows with the database.

WARNING! This wiki is not up-to-date. I'm currently working on the documentation.

Help

• Getting help

Installation

See the README

For the impatient

• Quick tutorial

Starting out

• Requirements
• Install
• Database setup
• Initial data loading

Workflows

Database management

• Get summary info
• Write tables
• Delete entries
• Check for loci overlap

General data retrieval

• Get a fasta (e.g. spacers, DRs, leaders, whole CRISPR loci)
• GFF3 of loci

Leader regions

If leader regions not known:

• Find and load leaders

If leader regions known:

• Load known leaders

CRISPR presence-absence

• subtype pres-abs ITOL metadata

Array BLAST (blastn of spacer and direct-repeats)

• Array blast
• Blast spacers
• Blast direct repeats (DRs)
• Get protospacers
• Get DNA template for crRNA (crDNA)
• Make protospacer-crDNA alignments
• Get the PAM regions
• Get protospacer-crDNA mismatches for the SEED region and total alignment

Plotting loci

• Plotting loci
• Make detailed comparative plots of CRISPR-CAS systems

Classifying subtype of arrays based on direct repeats

• Classify arrays

How do I...?

• HowTo