File	Date	Author	Commit
3rdParty	2016-05-11	Shyam Saladi	[aa9428] Remove c/cpp object files and ignore them in th...
DBOperation	2016-05-12	Shyam Saladi	[aa2c49] Change all ''' to """ to make consistent throug...
DesignOfExperiments	2016-05-12	Shyam Saladi	[aa2c49] Change all ''' to """ to make consistent throug...
Features	2016-05-12	Shyam Saladi	[2fa4a2] code formatting mostly
Utils	2016-05-12	Shyam Saladi	[02ca33] additional files (comment same as previous commit)
tests	2016-05-12	Shyam Saladi	[2fa4a2] code formatting mostly
tutorial	2016-05-11	Shyam Saladi	[c619ab] Move class diagram to tutorials folder
.gitignore	2016-05-12	Shyam Saladi	[693e83] Move data for test files into tests directory. ...
Data.py	2016-05-12	Shyam Saladi	[aa2c49] Change all ''' to """ to make consistent throug...
Functions.py	2016-05-12	Shyam Saladi	[2fa4a2] code formatting mostly
LICENSE	2013-06-17	jcg	[d41d8f] Initial commit for D-Tailor v1.0
README	2013-06-17	jcg	[d41d8f] Initial commit for D-Tailor v1.0
SequenceAnalyzer.py	2016-05-12	Shyam Saladi	[aa2c49] Change all ''' to """ to make consistent throug...
SequenceDesigner.py	2016-05-12	Shyam Saladi	[aa2c49] Change all ''' to """ to make consistent throug...
Solution.py	2016-05-12	Shyam Saladi	[2fa4a2] code formatting mostly
__init__.py	2013-06-17	jcg	[0710b6] Initial commit for D-Tailor v1.0
cleanFolders.sh	2016-05-11	Shyam Saladi	[b899fa] move clean tmp folder script

Read Me

D-Tailor v1.0
by Joao C Guimaraes, Miguel Rocha, Adam P Arkin and Guillaume Cambray
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1. Installing D-Tailor

1.1. Prerequisites

D-Tailor is implemented in Python. Python is an interpreted and interactive object-oriented programming language that is available for several platforms including Unix, Mac OSX and Microsoft Windows. Before starting to use D-Tailor, you need to install Python version 2. More information can be found at http://www.python.org.

D-Tailor uses a few command line utilities such as cat or awk that are commonly available for Unix or Unix-derived operating systems. When using Microsoft Windows it may be necessary to run D-Tailor in a Unix-emulation environment such as Cygwin (http://www.cygwin.com/).

To have access to certain functionalities in D-Tailor, you will need to install third-party software to predict RNA structure (UNAFold v3.6 and RNAplfold v1.6) and transcription terminators (TransTermHP v2.08). The sources for these tools are located in the folder “3rdParty” and, after installation, the compiled binaries must be copied to each corresponding folder. For installation instructions, please refer to the respective websites:
  - UNAFold — http://mfold.rna.albany.edu/?q=DINAMelt/software
  - RNAplfold (Vienna RNA package) — http://www.tbi.univie.ac.at/~ivo/RNA/
  - TransTermHP — http://transterm.cbcb.umd.edu/

All these tools are optional and hence only necessary if the user wants to use above-mentioned functionalities, namely predict RNA structure or transcription terminators. 

1.2. Installation

D-Tailor is a Python project ready to be used. To start using D-Tailor, simply download it from http://genomics.lbl.gov/~jcg/dtailor/ and copy the files to the destination folder.

1.3. License

D-Tailor is licensed under the BSD 2-Clause License.


2. D-Tailor tutorial

For detailed documentation please see tutorial/dtailor_tutorial.PDF