Biopython Free bioinformatics Python applications and libraries package
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parse library research bioinformatics library bioinformatics parser bioinformatics research

Biopython Description

Free bioinformatics Python applications and libraries package Biopython is a distributed collaborative effort to develop free Python applications and libraries which address the needs of current and future work in bioinformatics.Biopython is a set of libraries to provide the ability to deal with “things” of interest to biologists working on the computer. In general this means that you will need to have at least some programming experience (in python, of course!) or at least an interest in learning to program. Biopython’s job is to make your job easier as a programmer by supplying reusable libraries so that you can focus on answering your specific question of interest, instead of focusing on the internals of parsing a particular file format (of course, if you want to help by writing a parser that doesn’t exist and contributing it to Biopython, please go ahead!). So Biopython’s job is to make you happy! Here are some key features of "Biopython": · The ability to parse bioinformatics files into python utilizable data structures · Files in the supported formats can be iterated over record by record or indexed and accessed via a Dictionary interface. · Code to deal with popular on-line bioinformatics destinations · Interfaces to common bioinformatics programs · A standard sequence class that deals with sequences, ids on sequences, and sequence features. · Tools for performing common operations on sequences, such as translation, transcription and weight calculations. · Code to perform classification of data using k Nearest Neighbors, Naive Bayes or Support Vector Machines. · Code for dealing with alignments, including a standard way to create and deal with substitution matrices. · Code making it easy to split up parallelizable tasks into separate processes. · GUI-based programs to do basic sequence manipulations, translations, BLASTing, etc. · Extensive documentation and help with using the modules, including this file, on-line wiki documentation, the web site, and the mailing list. · Integration with BioSQL, a sequence database schema also supported by the BioPerl and BioJava projects. Requirements: · Python 2.3 or later · NumPy What's New in This Release: · Tiago Antao’s work on the Population Genetics module brings a command line wrapper for GenePop which allows the estimation of F-statistics, null allele frequencies and migration rates as well as tests for isolation by distance (IBD) and deviation from Hardy-Weinberg equilibrium. · Bio.SeqIO and Bio.AlignIO both now have a new convert() function that allows for simple (and potentially optimized) conversion between file formats. Bio.SeqIO also gets a new index() function which allows random access to sequences in a file without reading every record in that file into memory. · The new release also adds command line wrappers for the EMBOSS versions of the PHYLIP phylogeny programs and the Novoalign assembler from NovaCraft – plus squashes a few minor bugs reported since 1.51 was released.

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