Bioinformatics · CS Atlas

01Overview

In 1970 Needleman and Wunsch published sequence alignment; in 1977 Sanger invented DNA sequencing, and read lengths and throughput kept climbing. The Human Genome Project began in 1990 and its draft appeared in 2001. The explosion of sequence data made algorithms indispensable to biology.

CRISPR gene editing and high-throughput sequencing accelerated data production further after 2012. In 2020 AlphaFold 2 pushed protein structure prediction to near-experimental accuracy at CASP14, showing what deep learning could do for discovery. Today bioinformatics works on terabytes of omics data with graph algorithms, hidden Markov models, alignment indexes and large-scale parallelism.

02History

1970
Needleman–Wunsch
Dynamic programming for biological sequence alignment.
1977
Sanger sequencing
Where DNA sequencing begins.
1990
The Human Genome Project
Large-scale collaboration.
2001
The human genome draft
Sequence data explodes.
2020
AlphaFold 2
A breakthrough in protein structure prediction.

03Core concepts

Sequence alignment

Find the best matches and gaps between two sequences.

Assembly

Stitch short reads into a whole genome.

Structure prediction

Infer a three-dimensional structure from an amino-acid sequence.

04Hands-on

Do it once — it beats reading it ten times

Align two short protein sequences with Needleman–Wunsch by hand and check against Biopython

Tick this once you have built it and written down what you learned; the topic is then marked as built.

05Self-check

Say it in your own words first, then open the answer. Whatever you cannot explain is what to review next.

Can you explain "Sequence alignment"?

Find the best matches and gaps between two sequences.

Can you explain "Assembly"?

Stitch short reads into a whole genome.

Can you explain "Structure prediction"?

Infer a three-dimensional structure from an amino-acid sequence.

What problem did it solve, and why was there nothing better at the time?

Go back to the history section: how was this done before, and what did it cost?

If you had to build it today, how would you break it down?

Use the hands-on task above: write a plan of at most three steps before you start.

06Key people

Michael Waterman

1942 –

Sequence analysis algorithms and bioinformatics.

John Jumper

1985 –

Core author of AlphaFold; Nobel Prize in Chemistry 2024.

07Further reading

Biological Sequence AnalysisDurbin, Eddy, Krogh & Mitchison · 1998
Highly Accurate Protein Structure Prediction with AlphaFoldJumper et al. · 2021