Giraffe: tool for a) detecting popular features in DNA sequence, b) creating
maps of those features, and c) performing sequence analysis.

Example: http://www.addgene.org:8800/

This software was written and copyrighted by Addgene, and released under the
MIT License. See LICENSE file. It is now maintained by Benjie Chen.

The software is mostly divided into two parts: a Django based service that
detects features within a sequence, and a set of JavaScript widgets that
visualize the sequence, features, digests, etc.

Visualization
-------------

You can use the two parts separately. I.e. you can just use the JavaScript
widget for visualizing and analyzing sequence and features. See HTML files in
the demo directory. Also README file in src/django/giraffe/analyze/static/js
describes how to use just the JavaScript plasmid drawing widget.

Feature Detection
-----------------

Requirement for Django service:

	gcc - part of the feature detection algorithm is in C
	python (2.7+)
	django (1.2+)
	BioPython (1.56) - ORF detection via BioPython
		(You don't need NumPy for BioPython)
	MySQL, and mysql-python module

Install Django service:

	git clone [email protected]:addgene/giraffe.git
	cd giraffe
	cd src/django/giraffe/blat/frags; gcc -O6 -o bin/frags frags.c

	mysql
	> DROP DATABASE giraffe;
	> CREATE DATABASE giraffe CHARACTER SET 'utf8'
	
	cd src/django/giraffe; python manage.py syncdb --noinput

Run test server:

	cd src/django/giraffe; python manage.py runserver

	Then visit "/"

	Click on "See an example" to see an example.

API:

	You can POST a sequence to "/blat/", with the following CGI variables:

		db=default&sequence=your_dna_sequence_here

	Then you will be redirected to a URL that looks like

		/blat/8de364690dbeb88d2ab63bd66861725539aa3204/default

	The "8de3...3204" string is the hash identifier for your sequence. You can
	use this hash identifier and this URL to retrieve features in the future
	(JSON format).

	Also, you can use the hash identifier with the JavaScript widgets. See demo
	directory. You can download the HTML files from the demo directory to your
	local computer, and load them in your browser. These files show how you can
	incorporate Giraffe sequence map and analyzer widgets in your web app.
	
How to build your own features database:

	To be added later.