Biopython

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Biopython


Biopython is a collection of Python tools for computational biology and bioinformatics. Biopython contains modules and classes to represent protein sequences, nucleic acid sequences and sequence annotations. Biopython tools can perform common operations such as transcription, translation, obtain complements, reverse complements, parsing, running BLAST etc. We can use Biopython modules to access online databases such as NCBI. Biopython modules can also be used for sequence alignment, phylogenetics, sequence motifs, protein structure etc.

The Spoken Tutorial Effort for Biopython has being contributed by Dr. Snehalatha Kaliappan with domain reviews done by faculty from Dept of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamilnadu.

Contents

Basic Level

1. Introduction to Biopython

  • Important features of Biopython.
  • Information regarding download and installation on Linux Operating System.
  • Create a sequence object for the given DNA strand.
  • Transcription of the DNA sequence to mRNA.
  • Translation of mRNA to a protein sequence.
  • Convert coding DNA strand to a template DNA strand by making use of reverse complement method.


2. Manipulating Sequences

  • Generate a random DNA sequence.
  • Slice the DNA sequence at specified locations.
  • Join the two sequences together to form a new sequence (Concatenate).
  • Find the length of the sequence.
  • Count the number of individual bases or part of string.
  • Find a particular base or part of the string.
  • Convert sequence object to mutable sequence object.


3. Parsing Data

  • Download FASTA and GenBank files from NCBI database website
  • Parse data files using functions in Bio.SeqIO module.
  • Use parse function (Bio.SeqIO. Parse()) to extract information such as sequence id's, sequence contained in the file and length of the sequence.
  • Use read function (Bio.SeqIO.read()) to read contents from a data file with a single record.


4. Writing Sequence Files

  • Create Sequence Record Objects.
  • Write sequence files using write function of Sequence Input/Output module( Bio.SeqIO.write())
  • Convert between sequence file formats.
  • Sort records in a file by length.


5. BLAST

  • Run BLAST for the query sequence over internet through NCBI BLAST service.
  • Use qblast function in NCBIWWW module to run blast for a nucleotide sequence.
  • Save the output xml file in home folder.
  • Parse the BLAST output (xml) file using functions available in Bio.Blast.Record module.

Contributors and Content Editors

Snehalathak