Cookbook Entries

The entries contained in the Cookbook category are designed to compliment the general help given in the Tutorial (PDF) with specific examples of problems that can be solved with the Biopython tools.

This collection of examples is a new effort for Biopython, so is currently a little short. If you have suggestions for topics, please raise them on the mailing lists. If you have some example code of your own to put forward for this cookbook collection, that’s even better. By sharing it hopefully the community can comment on your code, and perhaps improve it, helping both you and future Biopython users.

Alternatively, are there any examples in the Tutorial (PDF) which you think would be worth copying (or moving) here? Let us know on the mailing lists.

Thanks

• Plotting ABI traces
• Represent an alignment from contig archived in ACE files.
• Retrieve and annotate Entrez Gene IDS with the Entrez module.
• Concatenating multiple alignments NEXUS files with the Bio.Nexus module.
• Converting sequence files with the Bio.SeqIO module.
• Mapping genetic coordinates with the Bio.SeqUtils.Mapper module.
• Methods for Degenerated Codons
• From gene sequence to predicted protein with the GFF module.
• Workflow to extract intergenic regions from a sequence.
• Bio.Phylo Cookbook.
• Reading data from UNIX pipes.
• Reading large PDB files with Biopython.
• Remove PDB disordered atoms with the Bio.PDB module.
• Retrieve nonmatching blast queries
• Sequence Cleaner
• Split large file