Name: phageParser
Owner: phageParser
Description: A project to extract CRISPR information from open genetic data.
Created: 2014-08-20 20:38:26.0
Updated: 2018-01-01 16:17:33.0
Pushed: 2018-01-20 02:13:36.0
Size: 25881
Language: Python
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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:
We will collect these annotations in a database that can users can query through a GUI (graphical user interface). Neither of these exist yet, and we are 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!
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.
When a virus enters a human body, specialized immune cells are often quick to recognize the virus invader and kill it. Bacteria do not have the benefit of millions of immune cells to protect them against viruses, but they have something else: CRISPR-Cas. The CRISPR-Cas immune response begins with the creation of spacer sequences from the invading virus' DNA followed by the production of small interfering crRNAs. Finally, when the bacterium is invaded again, the crRNAs recognize and cut the viral DNA, preventing infection.
Bacteria store their acquired spacers in their own DNA. The spacers are flanked by short pieces of bacterial DNA called repeats (see figure below).
Amazingly, CRISPR-Cas immunity is both adaptive and hereditary! After acquiring a spacer, bacteria are both protected against future virus attacks and they can pass on their spacer libraries to their descendants.
More research is needed to better understand how bacteria 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.
CRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity: a very good review paper on the CRISPR-cas system, the biological backdrop of this project.
You can download the source code of the project by git:
git clone https://github.com/phageParser/phageParser.git
After getting the local copy of the project, it is generally a good idea to create an isolated environment that belongs to the project and its specific packages. For this, python has a tool called virtualenv that can help create a python instance that has different packages than the system's version. To get started:
Make sure you have python3 in your system, if not, you can download python3 via their website
You can then install virtualenv package by pip
pip install virtualenv
For creating a virtualenv with a specific python version, you can supply the
path of the python binary as an argument. The virtual python instances are conventionally
kept in one place, usually in ~/.virtualenvs
. You can create the folder and make
an environment for phageParser as such:
mkdir ~/.virtualenvs && cd "$_"
python3 -m venv ~/.virtualenvs/pparserdev
You now have a separate environment which you can use to contribute
phageParser. Whenever you're developing for phageParser, use the following command
to activate the environment:
source ~/.virtualenvs/pparserdev/bin/activate
To install the required libraries for phageParser, after heading to the project folder
containing requirements.txt
, activate the project environment and run the following command:
pip install -r requirements.txt
For viewing the database, we recommend the Firefox SQLite Manager plugin. Once installed, launch it from the 'Tools' menu in Firefox.