Bioinformatics with python

• Biopython
• Scikit-Bio
• Biotite

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What is BioPython
for installing biopython:
pip install biopython or
conda install -c conda-forge biopython

Applications:

• For sequence analysis (DNA,RNA)
• To do transcription and translation of DNA (Protein Synthesis)
• Querying and Access Bioinformatic Databases
  • Entrez, BLAST, GenBank,etc
• 3D Structure analysis

Questions:

• How to create a sequence?
• Protein Synthesis (Transcription,Translation)
• Find GC content
• Molecular weights of a protein or DNA
• Convert protein sequence from one-letter to three-letter code and vice versa
• Find patterns
• How to find the Frequency of Nucleotide, Amino Acids,etc
• Sequence Alignment
• Similarity and homology

- Features of BioPython

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What is Biotite

• Biotite can handle a major part of the typical workflow for sequence and biomolecular structure data:
• Searching and fetching data from biological databases
• Reading and writing popular sequence/structure file formats
• Analyzing and editing sequence/structure data
• Visualizing sequence/structure data
• Interfacing external applications for further analysis

Modules of Biotite

• Sequence
• Structure
• Applications
• Database

Installation

pip install biotite

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What is Scikit-bio

Features

• Handling sequences: (skbio.io,skbio.sequence,skbio.alignment)
• Phylogenetics: (skbio.tree)
• Workflow Constructio
• State and Calculation: (skbio.stats,skbio.diversity)
• Metadata and Utility functionality: (skbio.metadata,skbio.util)

Installation

pip install scikit-bio