Biopython: Tutorial and Cookbook
Thegoal of Biopython is to make it as easy as possible to use Python for bioinformatics by creating high-quality, reusable modules and classes.
Biopython features include parsers for various Bioinformatics file formats (BLAST, Clustalw, FASTA, Genbank,...), access to online services (NCBI, Expasy,...), interfaces to commonand not-so-common programs (Clustalw, DSSP, MSMS...), a standard sequence class, various clusteringmodules, a KD tree data structure etc.
Table of contents
- Introduction
- Quick Start - What can you do with Biopython?
- Sequence objects
- Sequence annotation objects
- Sequence Input/Output
- Multiple Sequence Alignment objects
- BLAST
- BLAST and other sequence search tools
- Accessing NCBI's Entrez databases
- Swiss-Prot and ExPASy
- Going 3D: The PDB module
- Bio.PopGen: Population genetics
- Phylogenetics with Bio.Phylo
- Sequence motif analysis using Bio.motifs
- Cluster analysis
- Supervised learning methods
- Graphics including GenomeDiagram
- KEGG
- Bio.phenotype: analyse phenotypic data
- Cookbook - Cool things to do with it
- The Biopython testing framework
- Advanced
- Where to go from here - contributing to Biopython
| Pages : | 360 |
| Size : | 3.0 MB |
| File type : | |
| Downloads: | 85 |
| Created: | 2022-02-01 |
| License: | Open Publication License |
| Author(s): | by Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, Michiel de Hoon, Peter Cock, Tiago Antao, Eric Talevich, Bartek Wilczy?ski |
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