Tutorials¶

Every page in this section is generated from a Jupyter notebook in the repository and re-executed with the Kotlin kernel each time the site is built, so the outputs you see are what the released library produces. Each page links back to its notebook if you would rather run it yourself - see Getting started for how to set up the Kotlin kernel.

Sequences¶

• Basic sequence - creating nucleotide and protein sequences and the operations that come with them.
• Sequence operations - complementing, transcribing, translating, and searching, including at scale.
• Nucleotides and residues - the NUC enum: IUPAC codes, molecular weights, and complements.
• Amino acids and proteins - building peptides and reading residue properties from the AminoAcid enum.
• Sequence IO - streaming FASTA and FASTQ records with NucSeqIO.

Genomes and annotations¶

• Genomic ranges - positions, intervals, flanking, intersection, and reading BED files.
• Feature tree (GFF) - parsing GFF3 into an immutable gene/transcript/exon tree, and mutating it.
• Genomic features - a tabular, DataFrame-backed view of the same annotation.
• MAF processing - coverage and identity from MAF alignments, exported as BED and wiggle.