The Bio-Web: Molecular and Cell Biology and Bioinformatics news, tools, books, resources and web applications development

The Bio-web Open Source Free Python CGI Scripts for Molecular Biology and Bioinformatics

Here are some Python and Biopython related scripts and resources - Free, Open Source Python CGI Scripts. The source code of most projects is freely available. If you use significant parts of this code for your own projects please give proper credit.

• The OLIGO LOCALIZER
  Localizes an oligonucleotide on a DNA sequence. Supports IUPAC ambiguous DNA alphabet.
  Source code
• DNA/Protein sequence cleaner
  Allows the easy cleaning (removal of unwanted spaces, slashes, numbers etc..) of sequences. Tipically useful when retrieving sequences from online databases. Also allows custom numbering of the input sequence.
  Source code
• The DNA/Protein sequence randomizer
  Basically this is an interface to the Python "random" module. Custom number of iterations allowed. Optionally cleans the input sequence with the sequence cleaner before randomization. Optionally formats the output sequence.
  Source code
• The DNA sequence Reverse Complement Tool
  You can reverse, complement or reverse-complement your sequence. The sequence is cleaned by default from non-GATC characters. Support for ambiguous DNA characters (IUPAC) is forthcoming.
  Source code

(Bio)Python Links

• The Python Official Home Page
• The BioPython Official Home Page
• CSB Toolbox
  CSB is a python framework for building applications in the domain of structural bioinformatics
• Instant Hacking: A simple "Getting Started" Python Tutorial by Magnus Lie Hetland
• Writing CGI Programs in Python, by Preston Landers
• Introduction to Programming using Python by the Pasteur Institute in Paris
  Mainly designed for Biologists. Teaches programming from scratch, aimed at non programmers.
• Regular Expression HOWTO
  This document is an introductory tutorial to using regular expressions in Python with the re module. It provides a gentler introduction than the corresponding section in the official Python Library Reference.
• ug's HTML & Python CGI pages: Forms
  Very handy reference for writing forms for python scripts
• Introduction to Event-Driven Programming
  A short, general and clear introduction to events-driven programming
• Thinking in Tkinter
  Excellent basic tutorial for Tkinter, a module that allows the construction of grafical interfaces for your python scripts
• Regular expressions generator, free online tool
  A nice web-based tool for building regular expressions. Provides code for regular expressions in all major scripting languages including python
• A Quick Guide for Developing Effective Bioinformatics Programming Skills
  An excellent quick start set of guidelines for developing Bioinformatics programming skills
• An introduction to style sheets
  Most important aspects covered from scratch