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Basic BioPython Training for Bioinformatics

Biopython is a Python package freely available for computational molecular biology. Biopython can parse Blast results (standalone and web); run biology related programs (blastall, clustalw, EMBOSS); deal with FASTA formatted files; parse GenBank files; parse PubMed, Medline and work with on-line resource; parse Expasy, SCOP, Rebase, UniGene, SwissProt; deal with Sequences; data classification (k Nearest Neighbors, Bayes, SVMs); Aligning sequences; CORBA interaction with Bioperl and BioJava; SQL database storage through BioSQL; Neural Networks; Genetic Algorithms; Hidden Markov Models; creating pretty PDF files for posters; format flat files with random access to entries; structural biology PDB, FSSP.

This basic Biopython course includes

  • Sequence manipulation using Biopython
  • Annotating sequences
  • Sequence alignments
  • BLAST
  • Accessing NCBI databases


SkillsFuture Credit Applicable for Individual

WDA Training Grant Applicable for Company

Course Code: CRS-N-0035566)

Course Booking

$298.00

Course Date

Course Time

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Course Cancellation/Reschedule Policy

We reserve the right to cancel or re-schedule the course due to unforeseen circumstances. If the course is cancelled, we will refund 100% to participants.
Note the venue of the training is subject to changes due to class size and availability of the classroom.
Note the minimal class size to start a class is 3 Pax.

Course Details

Module 1 Introduction to Biopython

  • What is Biopython?
  • Biopython packages
  • Installing Biopython
  • Biopython website & resources


Module 2 Working with Sequences

  • Parsing
  • Slicing
  • Adding
  • Concatenating
  • Reverse complementing


Module 3 Annotating Sequences

  • FASTA record
  • GenBank record
  • Chromosomal Location
  • Sequence type


Module 4 Working with Sequence files

  • Parsing a file
  • Reading from a file
  • Writing to file
  • Converting file formats


Module 5 Sequence Alignment

  • Parsing an alignment file
  • Reading an alignment file
  • Writing alignments to file
  • Converting file formats
  • Manipulating alignments


Module 6 BLAST

  • What is BLAST?
  • Running BLAST
  • Parsing BLAST output
  • Searching within BLAST output


Module 7 Accessing Entrez Databases at NCBI

  • Connect to Entrez
  • List accessible Entrez Databases
  • Search Entrez Databases
  • Upload identifiers for searching
  • Return search results
  • Parsing results


Module 8 Simple Plotting (optional)

  • Plot %GC 
  • Plot sequence similarity (nucleotide dot plot)
  • Plot quality scores of sequencing reads

Who Should Attend

  • Biologists who want to learn basic bioinformatics
  • Bioinformatics Scientists who want basic training in Biopython

Prerequisite

  • Basic programming skills
  • Molecular biology
  • Basic bioinformatics (useful but not essential)

Trainers

BioPython TrainerDr. Marie Wong has a BSc (Biochemistry and Molecular Biology) from the University of Melbourne and a PhD (Structural Biology) from the University of Singapore. She has had more than 18 years in the field of Bioinformatics in both academic and industrial settings.

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