Metadata-Version: 1.1
Name: reoptimize
Version: 0.1.0a2
Summary: A tool to optimize reaction conditions for restriction enzyme digests of DNA
Home-page: https://github.com/mjeltsch/reoptimize
Author: Michael Jeltsch
Author-email: michael@jeltsch.org
License: GPLv3
Description: reoptimize
        ==========
        
        Python tool to optimize reaction conditions for restriction enzyme
        digests of DNA
        
        This tools lets you search for a suitable buffer for a simultaneous
        digest of DNA using an arbitrary number of enzymes. It calculates the
        amount of enzymes needed (in units) and takes into account the duration
        of the restriction digest (based on the NEB data on enzyme survival and
        time saver qualification). It's a very crude first attempt, but it's
        going to improve slowly according to how much time we have. Planned are
        also GUI interfaces for Linux, macOS and Windows.
        
        Inputs needed:
        --------------
        
        1. Enzyme name(s)
        2. How many cuts does the target DNA have for each selected enzyme?
           (optional, default 1)
        3. How long is the target DNA (in base pairs)? (optional, default 5000)
        4. How long are you going to incubate the reaction (in hours)?
           (optional, default 1 hour)
        5. How much DNA do you want to cut (in µg)? (optional, default 1 µg)
        
        Output:
        -------
        
        1. Possible buffers in the order of suitability (or the result
           "simultaneous digest not recommended")
        2. Amount of each enzyme needed for all possible buffers
        
        Requirements:
        -------------
        
        biopython
        
        Since even the latest Biopython distribution doesn't contain all enzymes
        sold by NEB, you need to manually update the Restriction\_Dictionary.py
        manually with the file Restriction\_Dictionary.py by copying it into the
        Bio/Restriction folder of the folder, where your python3 stores the
        python packages. On Ubuntu 16.04, this would be
        /usr/lib/python3/dist-packages/Bio/Restriction.
        
        Files:
        ------
        
        *reoptimize.py* The script that does the calculations. Usage examples:
        
        This is a double digest with AflIII and HindIII, where the target DNA
        has two AflIII sites and one HindIII site:
        
            reoptimize -e 'AflIII 2' 'HindIII 1'
        
        This gives all necessary parameters via the command line:
        
            reoptimize -e 'EcoRI 2' 'HindIII 3' -l 3000 -t 4 -m 2
        
        -l (length of target dna, in base pairs) -t (incubation time, in hours)
        -m (amount of DNA, in µg)
        
        *make\_sqlite\_database.py* This script fetches all the data for NEB
        enzymes from the NEB web pages and assembles the database that is needed
        for the script to run. Running it results in the database file
        "REsqlite3.db"
        
        *assay\_DNAs.fasta* This files contains the full DNA sequences of all
        assay DNAs used by NEB. We include it here to avoid querying the
        "Frequency of restriction sites" table (which is anyway incomplete).
        
Keywords: DNA,restriction enzymes,recombinant DNA technology
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
