Technology or method
Bioinformatics
Using computers to store, search and analyze biological data such as DNA and protein sequences.
Bioinformatics
Computing with biological data.
Bioinformatics uses computers to make sense of biological data, such as the letters of DNA.
Bioinformaticians align sequences, search databases, assemble genomes and predict protein structures.
Core methods include dynamic-programming alignment, heuristic search with BLAST, substitution matrices, public databases such as GenBank, UniProt and the Protein Data Bank, and structure prediction with AlphaFold.
Big questions
- How do we find a gene's relatives in a database?
- How do you compare two sequences fairly?
- Can a computer predict a protein's shape?
Key ideas
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Technology or method
Sequence alignment
Lining up DNA or protein sequences to find similarities. Dynamic programming finds the best global or local alignment.
Technology or method
BLAST
A fast heuristic tool for finding similar sequences in large databases.
Idea or model
Substitution matrices
Scores for replacing one amino acid with another, such as BLOSUM, used when aligning proteins.
Technology or method
Biological databases
Public archives such as GenBank for sequences, UniProt for proteins and the Protein Data Bank for structures.
Technology or method
Protein structure prediction
Predicting a protein's three-dimensional shape from its sequence. AlphaFold made accurate predictions possible for many proteins.
Idea or model
Human genome
The full DNA sequence of a human. Drafts were published in 2001, and the first gap-free sequence in 2022.
Technology or method
DNA sequencing
Reading the order of the bases in DNA, from single genes to whole genomes.
Also in Bioinformatics
Explore it in the labs
Literature search
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- Bioinformatics
- Molecular Biology
- Ecology
Simulation
Pair bases, follow a real human gene from DNA to protein, make mutations, and predict inheritance with Punnett squares.
- Genetics
- Molecular Biology
- Biochemistry
Timeline and explorer
A sourced timeline from the double helix to CRISPR therapies, eight technologies labeled established or emerging, and a PCR model.
- Biotechnology
- Synthetic Biology
- Genetics
Current research
Search published papers and preprints in Bioinformatics, with clear labels for reviews, primary research, clinical trials and preprints.
Search papers in BioinformaticsSources & further reading
The explanations on this page are our own summaries of these sources. Follow a link to read the original; if anything here disagrees with it, the original wins. How we choose and check sources.
Bioinformatics (opens the original in a new tab)
National Human Genome Research Institute. Talking Glossary of Genomic and Genetic Terms. National Human Genome Research Institute, NIH.
ReferenceGovernment sourceEducationalBasic local alignment search tool (opens the original in a new tab)
Altschul SF, Gish W, Miller W, et al. (1990). Journal of Molecular Biology 215:403-410.
BLAST, the fast heuristic search used to compare sequences against databases.
Peer-reviewedPrimary researchUniProt: the Universal Protein Knowledgebase in 2023 (opens the original in a new tab)
UniProt Consortium (2023). Nucleic Acids Research 51:D523-D531.
Peer-reviewedPrimary researchHighly accurate protein structure prediction with AlphaFold (opens the original in a new tab)
Jumper J, Evans R, Pritzel A, et al. (2021). Nature 596:583-589.
Peer-reviewedPrimary researchA general method applicable to the search for similarities in the amino acid sequence of two proteins (opens the original in a new tab)
Needleman SB, Wunsch CD (1970). Journal of Molecular Biology 48:443-453.
Dynamic programming for global sequence alignment.
Historical paperPrimary researchIdentification of common molecular subsequences (opens the original in a new tab)
Smith TF, Waterman MS (1981). Journal of Molecular Biology 147:195-197.
Dynamic programming for local sequence alignment.
Peer-reviewedPrimary researchAmino acid substitution matrices from protein blocks (opens the original in a new tab)
Henikoff S, Henikoff JG (1992). Proceedings of the National Academy of Sciences 89:10915-10919.
Peer-reviewedPrimary researchGenBank Overview (opens the original in a new tab)
National Center for Biotechnology Information. ncbi.nlm.nih.gov. National Library of Medicine, NIH.
DatabaseGovernment sourceThe Protein Data Bank (opens the original in a new tab)
Berman HM, Westbrook J, Feng Z, et al. (2000). Nucleic Acids Research 28:235-242.
Peer-reviewedPrimary researchAlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models (opens the original in a new tab)
Varadi M, Anyango S, Deshpande M, et al. (2022). Nucleic Acids Research 50:D439-D444.
Peer-reviewedPrimary researchInitial sequencing and analysis of the human genome (opens the original in a new tab)
Lander ES, Linton LM, Birren B, et al. (2001). Nature 409:860-921.
Peer-reviewedPrimary researchThe sequence of the human genome (opens the original in a new tab)
Venter JC, Adams MD, Myers EW, et al. (2001). Science 291:1304-1351.
Peer-reviewedPrimary researchThe complete sequence of a human genome (opens the original in a new tab)
Nurk S, Koren S, Rhie A, et al. (2022). Science 376:44-53.
The Telomere-to-Telomere consortium's gapless human genome assembly.
Peer-reviewedPrimary researchDNA sequencing with chain-terminating inhibitors (opens the original in a new tab)
Sanger F, Nicklen S, Coulson AR (1977). Proceedings of the National Academy of Sciences 74:5463-5467.
Peer-reviewedPrimary research