{ "info": { "author": "Michael Jeltsch", "author_email": "michael@jeltsch.org", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Intended Audience :: Science/Research", "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", "Programming Language :: Python :: 3", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Scientific/Engineering :: Chemistry", "Topic :: Scientific/Engineering :: Medical Science Apps." ], "description": "reoptimize\n==========\n\nPython tool to optimize reaction conditions for restriction enzyme\ndigests of DNA\n\nThis tools lets you search for a suitable buffer for a simultaneous\ndigest of DNA using an arbitrary number of enzymes. It calculates the\namount of enzymes needed (in units) and takes into account the duration\nof the restriction digest (based on the NEB data on enzyme survival and\ntime saver qualification). It's a very crude first attempt, but it's\ngoing to improve slowly according to how much time we have. Planned are\nalso GUI interfaces for Linux, macOS and Windows.\n\nInputs needed:\n--------------\n\n1. Enzyme name(s)\n2. How many cuts does the target DNA have for each selected enzyme?\n (optional, default 1)\n3. How long is the target DNA (in base pairs)? (optional, default 5000)\n4. How long are you going to incubate the reaction (in hours)?\n (optional, default 1 hour)\n5. How much DNA do you want to cut (in \u00b5g)? (optional, default 1 \u00b5g)\n\nOutput:\n-------\n\n1. Possible buffers in the order of suitability (or the result\n \"simultaneous digest not recommended\")\n2. Amount of each enzyme needed for all possible buffers\n\nRequirements:\n-------------\n\nbiopython\n\nSince even the latest Biopython distribution doesn't contain all enzymes\nsold by NEB, you need to manually update the Restriction\\_Dictionary.py\nmanually with the file Restriction\\_Dictionary.py by copying it into the\nBio/Restriction folder of the folder, where your python3 stores the\npython packages. On Ubuntu 16.04, this would be\n/usr/lib/python3/dist-packages/Bio/Restriction.\n\nFiles:\n------\n\n*reoptimize.py* The script that does the calculations. Usage examples:\n\nThis is a double digest with AflIII and HindIII, where the target DNA\nhas two AflIII sites and one HindIII site:\n\n reoptimize -e 'AflIII 2' 'HindIII 1'\n\nThis gives all necessary parameters via the command line:\n\n reoptimize -e 'EcoRI 2' 'HindIII 3' -l 3000 -t 4 -m 2\n\n-l (length of target dna, in base pairs) -t (incubation time, in hours)\n-m (amount of DNA, in \u00b5g)\n\n*make\\_sqlite\\_database.py* This script fetches all the data for NEB\nenzymes from the NEB web pages and assembles the database that is needed\nfor the script to run. Running it results in the database file\n\"REsqlite3.db\"\n\n*assay\\_DNAs.fasta* This files contains the full DNA sequences of all\nassay DNAs used by NEB. We include it here to avoid querying the\n\"Frequency of restriction sites\" table (which is anyway incomplete).\n\n\n", "description_content_type": null, "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/mjeltsch/reoptimize", "keywords": "DNA,restriction enzymes,recombinant DNA technology", "license": "GPLv3", "maintainer": "", "maintainer_email": "", "name": "reoptimize", "package_url": "https://pypi.org/project/reoptimize/", "platform": "", "project_url": "https://pypi.org/project/reoptimize/", "project_urls": { "Homepage": "https://github.com/mjeltsch/reoptimize" }, "release_url": "https://pypi.org/project/reoptimize/0.1.0a2/", "requires_dist": [ "biopython", "click" ], "requires_python": "", "summary": "A tool to optimize reaction conditions for restriction enzyme digests of DNA", "version": "0.1.0a2" }, "last_serial": 3139801, "releases": { "0.1.0a1": [ { "comment_text": "", "digests": { "md5": "2ad0c6c28480046f9d4fddc0f91b3203", "sha256": "413afaef64ff5b64550b0700b355b8a46a88c9dbd7f75edf5ca49dd16a108f13" }, "downloads": -1, "filename": "reoptimize-0.1.0a1-py3-none-any.whl", "has_sig": false, "md5_digest": "2ad0c6c28480046f9d4fddc0f91b3203", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 258108, "upload_time": "2017-08-29T08:29:04", "url": "https://files.pythonhosted.org/packages/d8/4c/d1b8f5f8839802ae62d7907f482ea4c415dbe8700e1353eae4206d61f670/reoptimize-0.1.0a1-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "b4c4f18292a6a2fb8a77447712b372f6", "sha256": "6f9c6521849700ed5f85275dc6bfecc265486ddb0c8665e11aa184bc039845eb" }, "downloads": -1, "filename": "reoptimize-0.1.0a1.tar.gz", "has_sig": false, "md5_digest": "b4c4f18292a6a2fb8a77447712b372f6", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 246015, "upload_time": "2017-08-29T08:29:07", "url": "https://files.pythonhosted.org/packages/25/22/54d0fed4c7276b27032689ebcc14a09852e2a40f13cfa4a085aa8f555b03/reoptimize-0.1.0a1.tar.gz" } ], "0.1.0a2": [ { "comment_text": "", "digests": { "md5": "1e3542ebcbf466fad847b672cfcd04b6", "sha256": "7ec44bbf4d3d49d6b2272884f9208e5cb4958a5499901c1c2916c2a5f32a8306" }, "downloads": -1, "filename": "reoptimize-0.1.0a2-py3-none-any.whl", "has_sig": false, "md5_digest": "1e3542ebcbf466fad847b672cfcd04b6", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 262860, "upload_time": "2017-09-01T07:59:20", "url": "https://files.pythonhosted.org/packages/34/32/a861166fc74a942c6601305df095a776952742db738d491c514aeb6663a7/reoptimize-0.1.0a2-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "451752f56b3c10c8ae5cfa083dd052bd", "sha256": "26ca181bf5aa91d394c916f416cab591dcd28d373450c0db634c7ae6963ae9f7" }, "downloads": -1, "filename": "reoptimize-0.1.0a2.tar.gz", "has_sig": false, "md5_digest": "451752f56b3c10c8ae5cfa083dd052bd", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 248839, "upload_time": "2017-09-01T07:59:22", "url": "https://files.pythonhosted.org/packages/32/4c/da06feaf1720e99bf5cdef563660d0548d3027aacd78d5d8903b3ce87221/reoptimize-0.1.0a2.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "1e3542ebcbf466fad847b672cfcd04b6", "sha256": "7ec44bbf4d3d49d6b2272884f9208e5cb4958a5499901c1c2916c2a5f32a8306" }, "downloads": -1, "filename": "reoptimize-0.1.0a2-py3-none-any.whl", "has_sig": false, "md5_digest": "1e3542ebcbf466fad847b672cfcd04b6", "packagetype": "bdist_wheel", "python_version": "py3", "requires_python": null, "size": 262860, "upload_time": "2017-09-01T07:59:20", "url": "https://files.pythonhosted.org/packages/34/32/a861166fc74a942c6601305df095a776952742db738d491c514aeb6663a7/reoptimize-0.1.0a2-py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "451752f56b3c10c8ae5cfa083dd052bd", "sha256": "26ca181bf5aa91d394c916f416cab591dcd28d373450c0db634c7ae6963ae9f7" }, "downloads": -1, "filename": "reoptimize-0.1.0a2.tar.gz", "has_sig": false, "md5_digest": "451752f56b3c10c8ae5cfa083dd052bd", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 248839, "upload_time": "2017-09-01T07:59:22", "url": "https://files.pythonhosted.org/packages/32/4c/da06feaf1720e99bf5cdef563660d0548d3027aacd78d5d8903b3ce87221/reoptimize-0.1.0a2.tar.gz" } ] }