BioPython About the Tutorial Biopython is an open-source python tool mainly used in bioinformatics field. This tutorial walks through the basics of Biopython package, overview of bioinformatics, sequence manipulation and plotting, population genetics, cluster analysis, genome analysis, connecting with BioSQL databases and finally concludes with some examples. Audience This tutorial is prepared for professionals who are aspiring to make a career in the field of bioinformatics programming using python as programming tool. This tutorial is intended to make you comfortable in getting started with the Biopython concepts and its various functions. Prerequisites Before proceeding with the various types of concepts given in this tutorial, it is being assumed that the readers are already aware about bioinformatics. In addition to this, it will be very helpful if the readers have a sound knowledge on Python. Copyright & Disclaimer Copyright 2018 by Tutorials Point (I) Pvt. Ltd. All the content and graphics published in this e-book are the property of Tutorials Point (I) Pvt. Ltd. The user of this e-book is prohibited to reuse, retain, copy, distribute or republish any contents or a part of contents of this e-book in any manner without written consent of the publisher. We strive to update the contents of our website and tutorials as timely and as precisely as possible, however, the contents may contain inaccuracies or errors. Tutorials Point (I) Pvt. Ltd. provides no guarantee regarding the accuracy, timeliness or completeness of our website or its contents including this tutorial. If you discover any errors on our website or in this tutorial, please notify us at [email protected] i BioPython Table of Contents About the Tutorial ............................................................................................................................................ i Audience ........................................................................................................................................................... i Prerequisites ..................................................................................................................................................... i Copyright & Disclaimer ..................................................................................................................................... i Table of Contents ............................................................................................................................................ ii 1. Biopython – Introduction .......................................................................................................................... 1 Features ........................................................................................................................................................... 1 Goals ................................................................................................................................................................ 1 Advantages ...................................................................................................................................................... 2 Sample Case Study .......................................................................................................................................... 2 2. Biopython – Installation ............................................................................................................................ 3 3. Biopython – Creating Simple Application .................................................................................................. 6 4. Biopython – Sequence .............................................................................................................................. 8 Alphabet Module ............................................................................................................................................. 8 Basic Operations ............................................................................................................................................ 10 5. Biopython – Advanced Sequence Operations.......................................................................................... 13 Complement and Reverse Complement ....................................................................................................... 13 GC Content .................................................................................................................................................... 14 Transcription ................................................................................................................................................. 14 Translation ..................................................................................................................................................... 14 6. Biopython – Sequence I/O Operations .................................................................................................... 17 SeqRecord ...................................................................................................................................................... 17 Parsing Sequence File Formats ...................................................................................................................... 17 FASTA ............................................................................................................................................................. 17 GenBank ........................................................................................................................................................ 19 7. Biopython – Sequence Alignments .......................................................................................................... 21 ii BioPython Parsing Sequence Alignment ......................................................................................................................... 21 Multiple Alignments ...................................................................................................................................... 22 Pairwise Sequence Alignment ....................................................................................................................... 23 Support for Sequence Alignment Tools ......................................................................................................... 25 8. Biopython – Overview of BLAST .............................................................................................................. 27 Running over Internet ................................................................................................................................... 27 Connecting and Searching ............................................................................................................................. 28 Running Standalone BLAST ............................................................................................................................ 30 Parsing BLAST Result ..................................................................................................................................... 33 9. Biopython – Entrez Database .................................................................................................................. 35 Database Connection Steps ........................................................................................................................... 35 Search Database ............................................................................................................................................ 37 Fetch Records ................................................................................................................................................ 39 10. Biopython – PDB Module ........................................................................................................................ 40 Protein Structure File Formats ...................................................................................................................... 40 mmCIF Parser ................................................................................................................................................ 40 PDB Parser ..................................................................................................................................................... 41 PDB Structure ................................................................................................................................................ 42 Model ............................................................................................................................................................ 42 Chain .............................................................................................................................................................. 43 Residue .......................................................................................................................................................... 43 Atoms ............................................................................................................................................................ 43 11. Biopython – Motif Objects ...................................................................................................................... 44 Creating Simple DNA Motif ..........................................................................................................................