Introduction to Biopython https://www.tutorialspoint.com/biopython/biopython_introduction.
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Biopython - Introduction
Biopython is the largest and most popular bioinformatics package for Python. It
contains a number of different sub-modules for common bioinformatics tasks. It is
developed by Chapman and Chang, mainly written in Python. It also contains C code
to optimize the complex computation part of the software. It runs on Windows, Linux,
Mac OS X, etc.
Basically, Biopython is a collection of python modules that provide functions to deal
with DNA, RNA & protein sequence operations such as reverse complementing of a
DNA string, finding motifs in protein sequences, etc. It provides lot of parsers to read
all major genetic databases like GenBank, SwissPort, FASTA, etc., as well as wrappers/
interfaces to run other popular bioinformatics software/tools like NCBI BLASTN,
Entrez, etc., inside the python environment. It has sibling projects like BioPerl,
BioJava and BioRuby.
Features
Biopython is portable, clear and has easy to learn syntax. Some of the salient features
are listed below −
Interpreted, interactive and object oriented.
Supports FASTA, PDB, GenBank, Blast, SCOP, PubMed/Medline, ExPASy-related
formats.
Option to deal with sequence formats.
Tools to manage protein structures.
BioSQL − Standard set of SQL tables for storing sequences plus features and
annotations.
Access to online services and database, including NCBI services (Blast, Entrez,
PubMed) and ExPASY services (SwissProt, Prosite).
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Access to local services, including Blast, Clustalw, EMBOSS.
Goals
The goal of Biopython is to provide simple, standard and extensive access to
bioinformatics through python language. The specific goals of the Biopython are listed
below −
Providing standardized access to bioinformatics resources.
High-quality, reusable modules and scripts.
Fast array manipulation that can be used in Cluster code, PDB, NaiveBayes and
Markov Model.
Genomic data analysis.
Advantages
Biopython requires very less code and comes up with the following advantages −
Provides microarray data type used in clustering.
Reads and writes Tree-View type files.
Supports structure data used for PDB parsing, representation and analysis.
Supports journal data used in Medline applications.
Supports BioSQL database, which is widely used standard database amongst
all bioinformatics projects.
Supports parser development by providing modules to parse a bioinformatics
file into a format specific record object or a generic class of sequence plus
features.
Clear documentation based on cookbook-style.
Sample Case Study
Let us check some of the use cases (population genetics, RNA structure, etc.,) and try
to understand how Biopython plays an important role in this field −
Population genetics is the study of genetic variation within a population, and involves
the examination and modeling of changes in the frequencies of genes and alleles in
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populations over space and time.
Biopython provides Bio.PopGen module for population genetics. This module contains
all the necessary functions to gather information about classic population genetics.
Three major biological macromolecules that are essential for our life are DNA, RNA
and Protein. Proteins are the workhorses of the cell and play an important role as
enzymes. DNA (deoxyribonucleic acid) is considered as the blueprint of the cell. It
carries all the genetic information required for the cell to grow, take in nutrients, and
propagate. RNA (Ribonucleic acid) acts as DNA photocopy in the cell.
Biopython provides Bio.Sequence objects that represents nucleotides, building blocks
of DNA and RNA.
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