Chapter 9 of Bioinformatics

Biological sequences and databases soon

DNA, RNA and protein sequences as data: Biopython, FASTA and other formats, pairwise alignment, and the ideas behind BLAST.

soon This chapter is planned and not yet written. The outline below is the current plan; it may change.

What it will cover

• Sequences as strings: alphabets, reverse complements, translation
• Biopython: SeqIO, SeqRecord and reading FASTA/GenBank
• Pairwise alignment: scoring matrices, gaps, dynamic programming
• Database search concepts: BLAST, E-values, sequence identity
• Fetching records from public databases responsibly
• Lab 9: build a small protein family dataset and cluster it by identity

Planned learning outcomes

1. Read, write and manipulate sequence files with Biopython.
2. Explain how pairwise alignment works and interpret an alignment score and an E-value.
3. Assemble a sequence dataset with identity-based clustering ready for machine learning.

In the meantime

Everything here builds on Part I, in particular the evaluation habits of Chapter 2. Episode 2.6 already introduces the group splits that become sequence-identity splits here.

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