What bioinformatics is

Bioinformatics uses computers, mathematics and statistics (and sometimes engineering) to store, find, analyse and interpret biological data. It overlaps with computational biology and biostatistics. An early milestone was Margaret Dayhoff's Atlas of Protein Sequence and Structure (1965); she also introduced the one-letter codes for amino acids still used today.

The NCBI (National Center for Biotechnology Information) in the USA hosts large databases of DNA sequences, proteins and research papers. GenBank, a public bank of DNA sequences, began in 1982. The field grew fast with the Human Genome Project and high-speed (high-throughput) sequencing.

Structural bioinformatics, studying the 3-D shapes of proteins (stored in the PDB), came first. Genome-wide informatics grew later, from about 2000.

Each laboratory technique produces its own kind of data:

• PCR makes many copies of a piece of DNA; qPCR measures how much RNA there is.
• Next-generation sequencing (NGS) gives millions of short sequences called reads, often stored in FASTQ files.
• Gel electrophoresis separates molecules by size and charge.
• HPLC separates small molecules (metabolites), giving chromatograms.
• Mass spectrometry gives mass spectra.

Common tools: BLAST (finds similar sequences); CLUSTAL, MAFFT and MUSCLE (line up several sequences: multiple sequence alignment); PHYLIP and PAUP (build family trees of evolution); GenScan (predicts genes); mfold (RNA shapes); Phyre2 (protein shapes). Statistics is done in R, SPSS, SAS and Excel.