Genome informatics and the Human Genome Project

A genome is an organism's complete DNA: all its genes and the regions between them. Genomics studies its structure, function and evolution. It sits alongside related "-omics" fields: transcriptomics (all RNAs), proteomics (all proteins) and metabolomics (all small molecules). Genome informatics turns genome-wide data into biological meaning.

Modern sequencing produces enormous amounts of data: the Broad Institute alone generates more than 24 terabytes of genome data a day.

The Human Genome Project, begun in the early 1990s, used Sanger's sequencing method. The public project (led by NHGRI) cut the genome into large pieces, copied them in bacteria (in bacterial artificial chromosomes), and sequenced them in order. The company Celera used a faster whole-genome shotgun approach: breaking the whole genome into random small pieces, sequencing them all, and letting computers put them together. The first draft appeared in 2001, and the project was declared complete in 2003.

The hardest parts to sequence and assemble were long repeated stretches of tightly packed DNA (heterochromatin) near the centromeres and telomeres, so some gaps remained after 2003.

Sequences are stored in standard text formats:

• FASTA: a header line starting with '>', then the sequence in one-letter codes.
• FASTQ: four lines per read: '@' plus the read's name; the sequence; a '+'; and a quality line with one character per base, showing how reliable each base call is, from '!' (lowest) to '~' (highest).