The Biopython Project is an international association of developers of freely available Python (https: \/\/www.python.org) tools for computational molecular biology. Python is an object oriented, interpreted, flexible language that is becoming increasingly popular for scientific computing. Python is easy to learn, has a very clear syntax and can easily be extended with modules written in C, C++ or FORTRAN.<\/p>\n
The Biopython web site (http:\/\/www.biopython.org) provides an online resource for modules, scripts, and web links for developers of Python-based software for bioinformatics use and research. Basically, the goal of Biopython is to make it as easy as possible to use Python for bioinformatics by creating high-quality, reusable modules and classes. Biopython features include parsers for various Bioinformatics file formats (BLAST, Clustalw, FASTA, Genbank,…), access to online services (NCBI, Expasy,…), interfaces to common and not-so-common programs (Clustalw, DSSP, MSMS…), a standard sequence class, various clustering modules, a KD tree data structure etc. and even documentation.<\/p>\n
Basically, we just like to program in Python and want to make it as easy as possible to use Python for bioinformatics by creating high-quality, reusable modules and scripts.<\/p>\n
The main Biopython releases have lots of functionality, including:<\/p>\n
\u2022 The ability to parse bioinformatics files into Python utilizable data structures, including support for the following formats:<\/p>\n
\u2022 Files in the supported formats can be iterated over record by record or indexed and accessed via a Dictionary interface.<\/p>\n
\u2022 Code to deal with popular on-line bioinformatics destinations such as:<\/p>\n
\u2022 Interfaces to common bioinformatics programs such as:<\/p>\n
\u2022 A standard sequence class that deals with sequences, ids on sequences, and sequence features.<\/p>\n
\u2022 Tools for performing common operations on sequences, such as translation, transcription and weight calculations.<\/p>\n
\u2022 Code to perform classification of data using k Nearest Neighbors, Naive Bayes or Support Vector Machines.<\/p>\n
\u2022 Code for dealing with alignments, including a standard way to create and deal with substitution matrices.<\/p>\n
\u2022 Code making it easy to split up parallelizable tasks into separate processes.<\/p>\n
\u2022 GUI-based programs to do basic sequence manipulations, translations, BLASTing, etc.<\/p>\n
\u2022 Extensive documentation and help with using the modules, including this file, on-line wiki documentation, the web site, and the mailing list.<\/p>\n
\u2022 Integration with BioSQL, a sequence database schema also supported by the BioPerl and BioJava projects.<\/p>\n
We hope this gives you plenty of reasons to download and start using Biopython!<\/p>\n","protected":false},"excerpt":{"rendered":"