Branches
The branches follow the kinds of data: sequence, structure, expression, and the databases that hold them together.
| Branch | What it works with | Typical question |
|---|---|---|
| Sequence analysis | DNA, RNA and protein sequences | What is this sequence, and what is it related to? |
| Genome assembly and annotation | Sequencing reads; finished genomes | Where are the genes in this new genome? |
| Variant analysis | Differences between a genome and the reference | Which of these variants could explain the disease? |
| Transcriptomics | RNA measurements across tissues, conditions or single cells | Which genes are switched on in this cell type? |
| Structural bioinformatics | Three-dimensional structures of proteins and nucleic acids | What shape does this protein fold into, and what binds to it? |
| Phylogenetics and comparative genomics | Aligned sequences from many species | How are these organisms related, and when did they diverge? |
| Proteomics and metabolomics | Mass-spectrometry measurements of proteins and small molecules | Which proteins are present, and how much of each? |
| Networks and systems biology | Interactions between genes, proteins and metabolites | What happens to the whole pathway if this gene is lost? |
| Databases and ontologies | The archives themselves, and the controlled vocabularies that describe them | How can two laboratories mean the same thing by the same word? |
The archives everything rests on
Public nucleotide sequences are held by three archives — in the United States, Europe and Japan — that exchange their data daily, so a sequence deposited in one appears in all. Protein structures have been collected in the Protein Data Bank since 1971; it opened with seven structures and now holds more than two hundred thousand.