{ "info": { "author": "Lasse Ebdrup Pedersen", "author_email": "laeb@biosustain.dtu.dk", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Environment :: Console", "Intended Audience :: Science/Research", "License :: Free for non-commercial use", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "# metmap\nDNA methyltransferase binding motif plasmid assembler\n\n## Overall purpose:\n* To identify the motifs of multiple DNA methyltransferases (DNA MTase) simultaneously.\n\n### Quick start\n* This script requires python 3.6 or newer.\n* Install using \"pip install metmap\"\n* This will put a script named \"run_metmap.py\" in your pythons bin folder.\n * Linux: You should just be able to type \"run_metmap.py\" from terminal\n * Windows: The script will be placed in your python folders \"Scripts\" subfolder and you can run it with \"python path\\to\\python\\Scripts\\run_metmap.py\" from command line\n * Mac: Who knows..probably works like linux?\n\n### Test\nYou can download the tests/test_data.txt and run \n```run_metmap.py test_data.txt``` \nThis should generate a cas1.fa and cas1.gb file.\n\n## Overview:\n* You have an organism with multiple identified DNA MTases and you wish to know their individual motifs.\n* You use NGS to obtain motifs of all methylated DNA sites.\n * Some of those motifs will contain ambiguous bases and some will not\n* You submit those motifs to this program\n* This program then stitches these motifs together in random order\n* Motifs may contain ambiguous bases per the IUPAC nucleotide code\n * We can't synthesize lots of ambiguous bases, so we \"de-ambigulate\" them before putting them into the final construct.\n * De-ambigulation happens according to 1 of 2 rules:\n * Rule 1:\n * Pick L random variants of the motif. E.g. Motif ATGNNTTA have a total of 16 possible actual sequences. If L<16 then the program will random pick L variants (without duplicates). If L>16 then each possible variant will be picked at least L/16 times and some will be picked 1 more than that.\n * Rule 2:\n * Make K copies of each completely \"de-ambigulated\" variant: E.g. the sequence \"SATC\" will then be treated as 2 sequences: \"GATC\" and \"CTAC\" that will each appear in K copies.\n* We put M N's between each motif\n* And the program will output P versions of these cassettes\n* You then clone this cassette into a plasmid with 1 DNA MTase in each plasmid.\n* You then transform this library into an organism that doesnt natively methylate DNA.\n* Grow, Harvest, Sequence plasmids.\n* ?\n* Profit! \n\n\n## Motif file format\n* The motifs should be stored in a standard text file\n* One motif per line, then a comma then a 1 or a 2 to indicate whether either rule 1 or 2 should be used for this motif\n Example: \n ATGCATGCATGC, 1 \n STGCAGTCATCGTTK, 1 \n ATCNNNNAAA, 2 \n CGTAGCANNNATCGATGC, 2 \n\n\n### IUPAC nucleotide code:\n|code | nucs|\n|:---:|:---:|\n|R|A or G|\n|Y|\tC or T \n|S|\tG or C \n|W|\tA or T \n|K|\tG or T \n|M|\tA or C \n|B|\tC or G or T \n|D|\tA or G or T \n|H|\tA or C or T \n|V|\tA or C or G \n|N|\tany base \n\n\n", "description_content_type": "text/markdown", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/cfblaeb/metmap", "keywords": "", "license": "", "maintainer": "", "maintainer_email": "", "name": "metmap", "package_url": "https://pypi.org/project/metmap/", "platform": "", "project_url": "https://pypi.org/project/metmap/", "project_urls": { "Homepage": "https://github.com/cfblaeb/metmap" }, "release_url": "https://pypi.org/project/metmap/1.0.4/", "requires_dist": [ "biopython" ], "requires_python": ">=3.6", "summary": "A tool for generating DNA MTase motif testing sequences", "version": "1.0.4" }, "last_serial": 4608013, "releases": { "1.0.3": [ { "comment_text": "", "digests": { "md5": "82b3cb1cfe5d22205fbee259218c9cba", "sha256": 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