phageParser is a project to extract and organize CRISPR information from open genetic data.

Many bacterial and archaeal genomes have been sequenced, and a large fraction of them have CRISPR systems, ranging from deadly human pathogens to archaea living in the harshest environments on earth. Some CRISPR systems have been studied very well, and more is being discovered about CRISPR every day. phageParser is a tool to collect this growing pool of information and generate versatile and useful annotations. These are some of the annotations we include:

• Spacer matches to known phages and prophages
• Phage genome content near spacer matches
• Spacer self-matches to host genome
• cas gene content and inferred CRISPR type

These annotations will be collected in a database that can be queried through a GUI. Neither of these exist yet, and we are actively looking for contributors.

This tool is currently in development, and it will always be possible to modify and enhance what is included as CRISPR research moves forward. We welcome suggestions for features or annotations you'd like to see! To suggest a feature, create an issue in our issue tracker.

phageParser is for anyone interested in exploring what we know about CRISPR systems in nature. This includes researchers, educators, and the general public.

We need many different skills and areas of expertise to build this tool, and you can help!

• Good first bugs include documentation and coding tasks that are doable by a newcomer. Mentoring is available for these tasks.
• Do you know about CRISPR biology? Issues labeled science are things we need people with science background to work on.
• Are you interested in contributing to project documentation? Any issues labeled documentation are ways to create or improve our docs.
• Do you know about databases? We're just starting to think about how to structure our data - join the discussion in issue #64.
• Do you know about Python and/or developing code? Check out our code-specific issues.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), and associated proteins (Cas) are part of the CRISPR-Cas system in bacteria. First observed in 1987 (Ishino et al., 1987), the CRISPR system is an adaptive immune system for bacteria.

In humans, when a virus enters the body, specialized immune cells are often quick to recognize the foreign pathogen and kill it. Bacteria do not have the benefit of a legion of cells to protect them against viruses, so they use the CRISPR-Cas mechanism that begins with the creation of spacer sequences from the invading virus' genetic material followed by the production of small interfering crRNAs. Finally, when the bacterium is invaded again, it uses the crRNAs to target the viral nucleic acid and prevent infection.

The spacers acquired are always flanked by bacterial DNA forming a library of small pieces of phage genomes from which to form crRNAs to target future viral genetic material (see Figure below).

Amazingly, after acquiring a spacer the bacteria are essentially vaccinated against future attacks and can pass on their phage libraries to future generations.

However, more research is needed to better understand the mechanisms that make this process possible, and to understand how microorganisms use their CRISPR systems in nature.

*Ishino, Y., Shinagawa, H., Makino, K., Amemura, M., and Nakata, A. (1987). Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J. Bacteriol. 169, 5429–5433.

##Relevant Literature

CRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity: a very good review paper on the CRISPR-cas system, the biological backdrop of this project.

##Installation

This package depends on Biopython, which can be installed as follows:

sudo make install-deps

##Usage

There are several usage options depending on what data outcome is desired.

###Usage - Blast individual bacteria files and get phage info from NCBI

• To get a phage dataset, take a fasta-formatted list of genes (example in data/velvet-distinct-spacers.fasta) and upload to http://phagesdb.org/blast/ - example result in data/blast-phagesdb.txt

• To clean up the results returned from phagesdb.org, you can call the Make target filter_by_expect, as in the example below.

make filter_by_expect infile=data/blast-phagesdb.txt output=output/ threshold=0.21

The result will be written to a file in output/, in a CSV formatted as

 Query, Name, Length, Score, Expect, QueryStart, QueryEnd, SubjectStart, SubjectEnd

with one header row (see #1 for discussion and details)

• To query NCBI for full genomes, do

 cat accessionNumber.txt | python acc2gb.py [email protected] > NCBIresults.txt

where accessionNumber.txt contains a list of accession numbers of interest; results will be dumped to NCBIresults.txt - see #2 for ongoing development here.

###Usage - Blasting multiple bacteria files and visualizing interactions

All of the following assumes you are using the reference CRISPR database set of spacers (file spacerdatabase.txt). Things should work with other spacer files; however there are several things hard-coded that might break. filterByExpect.py assumes the header line for each spacer is a number, for example, and bac_name is hardcoded in interactions.py as the 8th to 16th characters of the file name.

• To get individual spacer files for each bacteria species in the reference set, run CRISPR_db_parser on with the input file spacerdatabase.txt (downloaded from the Utilities page of CRISPRdb). The output files will be saved in the folder data/spacers.

• Make folders data/phages and /output. The current files in data/spacers and data/phages are examples.

• Blasting of spacer-containing files against the phage database can be done locally (handy if you have many files to blast). Download a local version of blast (blast+) here and find/follow instructions for your OS. (We used these instructions for Windows successfully.) Put the file Mycobacteriophages-All.fasta (in data folder) into the main blast+ directory and use the command makeblastdb -in "Mycobacteriophages-All.fasta" -dbtype nucl -title PhageDatabase -out phagedb to create a blast-ready database. It's possible to combine multiple databases into one blastable database by including more than one filename between the quotes in the -in command (i.e. the ENA phage database or NCBI virus database). Now you should be able to run the script BLAST_loop.py, but make sure directory names are correct - probably BLAST_loop.py will need to be run from inside wherever you installed blast+.

• run filterByExpectPhages.py, which essentially runs filterByExpect.py on all files in the /phages folder. These will be saved to /output.

• make a directory called sorted under output. run orderByExpect.py, which rearranges the results of filterByExpectPhages in each file to be in order of lowest to highest expect value.

• run interactions.py, which makes a json file json.txt for visualization in cytoscape.js.

Visualization

####Install Front-End Dependencies (to visualize in browser).

• Install node.js. Installing node will also install the node package manager (NPM).

• Install bower

• paste the contents of json.txt into the elements[] field in the file ui.js. This creates the structure needed for cytoscape.js to plot stuff. Various style fields can be changed, see cytoscape.js for documentation (or ask @MaxKFranz for help).

• paste the file index.html into a web browser.

###Usage - Detecting CRISPR type from bacterial genome metadata

• Start with a list of bacteria of interest - in this case, it's all the bacteria from CRISPRdb that had hits to a conglomerate of phage databases - bac_accession_list.txt.

• Next is to fetch bacterial genome data from NCBI. Run the following:

 cat bac_accession_list.txt | python acc2gb.py [email protected] > NCBIresults.txt

Be warned that this will take a long time (~1-2 hours) because the list is long. For testing, shorten the list to only a few accession numbers.

• Run the script trimGenbankDNA.py to get rid of unnecessary data and make the file size more manageable.

• Run cas_in_gb.pl (it's in Perl) to detect which Cas genes are in each organism.