Editing Biopython (section)

=== Genome diagrams ===

[[File:PKPS77.png|thumb|300px|Figure 3: A diagram of the genes on the pKPS77 plasmid,<ref name="NC_023330.1">{{cite web |url=https://www.ncbi.nlm.nih.gov/nuccore/NC_023330.1 |title=Klebsiella pneumoniae strain KPS77 plasmid pKPS77, complete sequence |date= |website= |publisher=NCBI |accessdate=10 September 2014}}</ref> visualised using the GenomeDiagram module in Biopython]]

The GenomeDiagram module provides methods of visualising sequences within Biopython.<ref name="Pritchard2006">{{Cite journal |last1=Pritchard |first1=Leighton |last2=White |first2=Jennifer A |last3=Birch |first3=Paul RJ |last4=Toth |first4=Ian K |title=GenomeDiagram: a python package for the visualization of large-scale genomic data |journal=Bioinformatics |date=March 2006 |volume=22 |issue=5 |pages=616–617 |doi=10.1093/bioinformatics/btk021 |pmid=16377612|doi-access=free }}</ref>  Sequences can be drawn in a linear or circular form (see Figure 3), and many output formats are supported, including [[Portable Document Format|PDF]] and [[Portable Network Graphics|PNG]].  Diagrams are created by making tracks and then adding sequence features to those tracks.  By looping over a sequence's features and using their attributes to decide if and how they are added to the diagram's tracks, one can exercise much control over the appearance of the final diagram.  Cross-links can be drawn between different tracks, allowing one to compare multiple sequences in a single diagram.