Metadata-Version: 1.1
Name: reoptimize
Version: 0.1.0a1
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 in a reaction). It's a very crude first
        attempt (and crashes immediately when you submit some wrongly formated data, inclu-
        ding capitalization), but it's going to improve slowly according to how much time
        we have. Planned are also GUI interfaces for Linux, macOS and Windows.
        
        ----
        
        Input needed:
        
        1. Enzyme name(s)
        2. How many cuts does the target DNA have for each selected enzyme?
        3. How long is the target DNA (base pairs)?
        4. How long are you going to incubate the reaction (hours)?
        5. How much DNA do you want to cut (microgram)?
        
        Output:
        
        1. Possible buffers in the order of suitability (or the result "simultaneous digest not recommended")
        2. Amount of each enzyme needed.
        
        ----
        
        Requirements:
        Biopython, click
        
        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.py digest -e 'AflIII 2' -e 'HindIII 1'
        
        
        This gives all necessary parameters via the command line:
        
        >./reoptimize.py digest -e 'EcoRI 2' -e '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 micrograms)
        
        If enzymes or other parameters are omitted, the program will prompt
        for them!
        
        
        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 dadabase 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
