Introduction to Biopython
Biopython is the most popular molecular biology package for computation. Brad Chapman and Jeff Chang developed it in 1999. It is mainly written in python but some C code is there to solve complex optimization. Biopython is capable of a lot like it can do protein structure, sequence motifs, sequence alignment also machine learning.
Biopython has a lot of libraries for the help of biologists in their work as it is portable, easy, and clear. In some cases Google images use Biopython, BioPerl, BioJAVA, BioRuby are the siblings of the Biopython project.
Reasons for development
- Creating high quality, reusable classes for the complex bio-informatics problems.
- Read genetic databases like Swissport, FASTA, and many more. After reading, it parse them to python utilizable data structure.
- For genomic data analysis.
- Tools for protein structure and have BigSQL-storing a lot of data.
- Good read and write for tree-view files.
- Support micro-array data type for clustering.
- Parsing bio-informatics files into a formalized object or in a generic class.
Sample Cases and Features
- RNA structure: RNA is one of the major macromolecules in our day-to-day life, others are DNA and Protein. DNA is called the blueprint of a cell and RNA acts as ‘DNA photocopy’ in the cell. For making this structural work easy Biopython has Bio.sequence object for DNA, RNA block representation.
- Genome Diagram: This module provides visualization of sequences in the PDF or JPG format. Multiple sequence compare is possible using this module.
- SeqRecord: Bio.sequence provides only the sequence. SeqRecord class provide name, description, feature along with the sequence.
- Population Genetics: It is the study of checking genetic variation in a population. It works with the examination, modeling of genes. Bio.PopGen module is there to simplify the work.
- Phylogeny: As I mentioned earlier Biopython has the advantage of using tree-view files. It uses Bio. Phylo module visualizing tree as well as manipulation and traversal from getting input in Newick, PhyloXML file format.
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