Metadata-Version: 1.1
Name: seguid_calculator
Version: 1.1.0
Summary: Calculates seguid, lseguid & cseguid checksums for biological sequences
Home-page: http://pypi.python.org/pypi/seguid_calculator
Author: Björn Johansson
Author-email: bjorn_johansson@bio.uminho.pt
License: LICENSE.txt
Description: 
        seguid_calculator
        =================
        
        |alt text|\ Seguid calculator is a small GUI application for calculating
        the SEGUID, lSEGUID and cSEGUID checksums for a biological sequence
        (DNA, RNA or protein). It is available as executables for Windows,
        MacOSX and Linux (see below).
        
        The SEGUID checksum is defined as the
        `SHA-1 <http://en.wikipedia.org/wiki/SHA-1>`__ cryptographic hash of a
        primary biological sequence in uppercase. SEGUID was suggested by
        `Babnigg and Giometti <http://www.ncbi.nlm.nih.gov/pubmed/16858731>`__
        as a way to provide stable identifiers of protein sequences in databases
        for cross referencing.
        
        There are several implementations of SEGUID calculation available, such
        as the one in `Biopython <http://biopython.org/wiki/Main_Page>`__.
        `Bio.SeqUtils.CheckSum <http://biopython.org/DIST/docs/api/Bio.SeqUtils.CheckSum-module.html>`__.
        See `slides <http://precedings.nature.com/documents/278/version/1>`__
        and the Biopython
        `wiki <http://www.biopython.org/wiki/SeqIO#Using_the_SEGUID_checksum>`__.
        See also this blog
        `post <http://wiki.christophchamp.com/index.php/SEGUID>`__ on the
        subject.
        
        The lSEGUID is the SEGUID of the lexocographically smallest of the sense
        or antisense strands of a double stranded DNA sequence. This means that
        if a sequence and its reverse compliment have the same lSEGUIDs. This
        can be useful to identify double stranded DNA sequences, regardless of
        the form they are presented.
        
        Circular SEGUID or cSEGUID is the SEGUID checksum for circular (DNA)
        sequences. As there are many circular permutations of a circular
        sequence, the use of the SEGUID checksum directly is impractical as
        there would be many checksums for the same sequence.The cSEGUID is the
        SEGUID of the `lexicographically minimal string
        rotation <http://en.wikipedia.org/wiki/Lexicographically_minimal_string_rotation>`__
        of a sequence or its reverse complement (whichever is
        `lexicographically <https://en.wikipedia.org/wiki/Lexicographical_order>`__
        smaller). The cSEGUID provide a unique and stable identifier for
        circular sequence, such as
        `plasmids <http://en.wikipedia.org/wiki/Plasmid>`__.
        
        Example
        -------
        
        The cSEGUID checksum can be useful to quickly determine if two sequences
        refer to the same vector. The sequence of the plasmid
        pFA6a-GFPS65T-kanMX6 is available from
        `Genbank <http://www.ncbi.nlm.nih.gov/nuccore/AJ002682>`__ and from
        other sources such as the `Forsburg
        lab <http://www-bcf.usc.edu/~forsburg/>`__, sequence
        `here <http://www-bcf.usc.edu/~forsburg/GFPS65T.html>`__ or
        `here <https://gist.github.com/BjornFJohansson/d394362134338d5f1ff0>`__.
        
        Both sequences are the same size and claim to describe the same vector,
        although the origins seem to have been set differently. Analysis of both
        sequences in seguid_calculator proves that both sequences are in fact
        representations of the same sequence by their identical cSEGUIDs:
        
        Genbank
        ^^^^^^^
        
        .. figure:: https://raw.githubusercontent.com/BjornFJohansson/seguid_calculator/master/genbank.png
           :alt: seguid_calculator
        
           alt text
        
        Forsburg
        ^^^^^^^^
        
        .. figure:: https://raw.githubusercontent.com/BjornFJohansson/seguid_calculator/master/forsburg.png
           :alt: seguid_calculator
        
           alt text
        
        Implementation
        --------------
        
        Seguid_calculator is written in python 2.7 with wxPython 3. Development
        happens on
        `Github <https://github.com/BjornFJohansson/seguid_calculator>`__ where
        source code is available.
        
        Executables
        -----------
        
        Executables are available for
        
        -  Windows 64 bit
        -  Mac OSX dmg and a zip file containing an app
        -  Linux deb package
        
        The executables can be downloaded from the button at the top of this
        page called
        `releases <https://github.com/BjornFJohansson/seguid_calculator/releases>`__.
        
        Visit the website `Bjorn Johansson’s group at
        CBMA <https://sites.google.com/site/metabolicengineeringgroup/>`__ for
        more information.
        
        Automatic build status
        ----------------------
        
        Windows standalone executables (32 and 64 bit) are built on
        `AppVeyor <https://ci.appveyor.com/project/BjornFJohansson/seguid-calculator>`__
        using `pyinstaller <http://www.pyinstaller.org/>`__ and
        `Miniconda <http://conda.pydata.org/miniconda.html>`__.
        
        |Build status|
        
        Standalone executables (64 bit) for MacOSX are built on
        `TravisCI <https://travis-ci.org/BjornFJohansson/seguid_calculator>`__
        using `pyinstaller <http://www.pyinstaller.org/>`__ and
        `Miniconda <http://conda.pydata.org/miniconda.html>`__.
        
        |Build Status|
        
        A debian package (.deb) is built offline, currently on Ubuntu 16.04
        using `stdeb <https://github.com/astraw/stdeb>`__. Look at the script
        “run_this_scritp_to_create_deb_package.sh”. This installs system
        shorcuts as well.
        
        .. |alt text| image:: https://raw.githubusercontent.com/BjornFJohansson/seguid_calculator/master/calculator.png
        .. |Build status| image:: https://ci.appveyor.com/api/projects/status/0bd4f7fi3g0m0itp?svg=true
           :target: https://ci.appveyor.com/project/BjornFJohansson/seguid-calculator
        .. |Build Status| image:: https://travis-ci.org/BjornFJohansson/seguid_calculator.svg?branch=master
           :target: https://travis-ci.org/BjornFJohansson/seguid_calculator
        
Keywords: bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Education
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
