{ "info": { "author": "Bj\u00f6rn Johansson", "author_email": "bjorn_johansson@bio.uminho.pt", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Environment :: Console", "Intended Audience :: Education", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Programming Language :: Python :: 2.7", "Topic :: Education", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "seguid_calculator\n=================\n\n|alt text|\\ Seguid calculator is a small GUI application for calculating\nthe SEGUID, lSEGUID and cSEGUID checksums for a biological sequence\n(DNA, RNA or protein). It is available as executables for Windows,\nMacOSX and Linux (see below).\n\nThe SEGUID checksum is defined as the\n`SHA-1 `__ cryptographic hash of a\nprimary biological sequence in uppercase. SEGUID was suggested by\n`Babnigg and Giometti `__\nas a way to provide stable identifiers of protein sequences in databases\nfor cross referencing.\n\nThere are several implementations of SEGUID calculation available, such\nas the one in `Biopython `__.\n`Bio.SeqUtils.CheckSum `__.\nSee `slides `__\nand the Biopython\n`wiki `__.\nSee also this blog\n`post `__ on the\nsubject.\n\nThe lSEGUID is the SEGUID of the lexocographically smallest of the sense\nor antisense strands of a double stranded DNA sequence. This means that\nif a sequence and its reverse compliment have the same lSEGUIDs. This\ncan be useful to identify double stranded DNA sequences, regardless of\nthe form they are presented.\n\nCircular SEGUID or cSEGUID is the SEGUID checksum for circular (DNA)\nsequences. As there are many circular permutations of a circular\nsequence, the use of the SEGUID checksum directly is impractical as\nthere would be many checksums for the same sequence.The cSEGUID is the\nSEGUID of the `lexicographically minimal string\nrotation `__\nof a sequence or its reverse complement (whichever is\n`lexicographically `__\nsmaller). The cSEGUID provide a unique and stable identifier for\ncircular sequence, such as\n`plasmids `__.\n\nExample\n-------\n\nThe cSEGUID checksum can be useful to quickly determine if two sequences\nrefer to the same vector. The sequence of the plasmid\npFA6a-GFPS65T-kanMX6 is available from\n`Genbank `__ and from\nother sources such as the `Forsburg\nlab `__, sequence\n`here `__ or\n`here `__.\n\nBoth sequences are the same size and claim to describe the same vector,\nalthough the origins seem to have been set differently. Analysis of both\nsequences in seguid_calculator proves that both sequences are in fact\nrepresentations of the same sequence by their identical cSEGUIDs:\n\nGenbank\n^^^^^^^\n\n.. figure:: https://raw.githubusercontent.com/BjornFJohansson/seguid_calculator/master/genbank.png\n :alt: seguid_calculator\n\n alt text\n\nForsburg\n^^^^^^^^\n\n.. figure:: https://raw.githubusercontent.com/BjornFJohansson/seguid_calculator/master/forsburg.png\n :alt: seguid_calculator\n\n alt text\n\nImplementation\n--------------\n\nSeguid_calculator is written in python 2.7 with wxPython 3. Development\nhappens on\n`Github `__ where\nsource code is available.\n\nExecutables\n-----------\n\nExecutables are available for\n\n- Windows 64 bit\n- Mac OSX dmg and a zip file containing an app\n- Linux deb package\n\nThe executables can be downloaded from the button at the top of this\npage called\n`releases `__.\n\nVisit the website `Bjorn Johansson\u2019s group at\nCBMA `__ for\nmore information.\n\nAutomatic build status\n----------------------\n\nWindows standalone executables (32 and 64 bit) are built on\n`AppVeyor `__\nusing `pyinstaller `__ and\n`Miniconda `__.\n\n|Build status|\n\nStandalone executables (64 bit) for MacOSX are built on\n`TravisCI `__\nusing `pyinstaller `__ and\n`Miniconda `__.\n\n|Build Status|\n\nA debian package (.deb) is built offline, currently on Ubuntu 16.04\nusing `stdeb `__. Look at the script\n\u201crun_this_scritp_to_create_deb_package.sh\u201d. This installs system\nshorcuts as well.\n\n.. |alt text| image:: https://raw.githubusercontent.com/BjornFJohansson/seguid_calculator/master/calculator.png\n.. |Build status| image:: https://ci.appveyor.com/api/projects/status/0bd4f7fi3g0m0itp?svg=true\n :target: https://ci.appveyor.com/project/BjornFJohansson/seguid-calculator\n.. |Build Status| image:: https://travis-ci.org/BjornFJohansson/seguid_calculator.svg?branch=master\n :target: https://travis-ci.org/BjornFJohansson/seguid_calculator", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "http://pypi.python.org/pypi/seguid_calculator", "keywords": "bioinformatics", "license": "LICENSE.txt", "maintainer": "", "maintainer_email": "", "name": "seguid-calculator", "package_url": "https://pypi.org/project/seguid-calculator/", "platform": "", "project_url": "https://pypi.org/project/seguid-calculator/", "project_urls": { "Homepage": "http://pypi.python.org/pypi/seguid_calculator" }, "release_url": "https://pypi.org/project/seguid-calculator/1.1.0/", "requires_dist": null, "requires_python": "", "summary": "Calculates seguid, lseguid & cseguid checksums for biological sequences", "version": "1.1.0" }, "last_serial": 4675632, "releases": { "1.1.0": [ { "comment_text": "", "digests": { "md5": "46e11031406ca5262aaaa22351256225", "sha256": "49c29ad9e6c6507b83451a7ed45e8b50ee41a7bb5d63695e654430790398baae" }, "downloads": -1, "filename": "seguid_calculator-1.1.0.zip", "has_sig": false, "md5_digest": "46e11031406ca5262aaaa22351256225", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 31925, "upload_time": "2019-01-09T07:00:10", "url": "https://files.pythonhosted.org/packages/b2/cf/3ca6e831ec6be9c2ce12d00d1230f469c3db30047ff4d98dd445a7fff17d/seguid_calculator-1.1.0.zip" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "46e11031406ca5262aaaa22351256225", "sha256": "49c29ad9e6c6507b83451a7ed45e8b50ee41a7bb5d63695e654430790398baae" }, "downloads": -1, "filename": "seguid_calculator-1.1.0.zip", "has_sig": false, "md5_digest": "46e11031406ca5262aaaa22351256225", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 31925, "upload_time": "2019-01-09T07:00:10", "url": "https://files.pythonhosted.org/packages/b2/cf/3ca6e831ec6be9c2ce12d00d1230f469c3db30047ff4d98dd445a7fff17d/seguid_calculator-1.1.0.zip" } ] }