Basic BioPython Training for Bioinformatics
Details
SkillsFuture Course - 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
Outline
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
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