DNA annotation

A visualization of Porphyra umbilicalis chloroplast genome annotation (GenBank accession: MF385003.1) made with Chloroplot.[1] The number of genes, the genome length, and the GC content are placed in the middle black circle. The outer gray circle shows GC content in the every section of the genome. All individual genes are placed on the outermost circle according to their position in the genome, their transcription direction and their length; they are color-coded based on the cellular function or component they are part of. Represented with arrows, the transcription directions for the inner and outer genes are listed clockwise and anticlockwise, respectively.

In molecular biology and genetics, DNA annotation or genome annotation is the process of describing the structure and function of the components of a genome,[2] by analyzing and interpreting them in order to extract their biological significance and understand the biological processes in which they participate.[3] Among other things, it identifies the locations of genes and all the coding regions in a genome and determines what those genes do.[4]

Annotation is performed after a genome is sequenced and assembled, and is a necessary step in genome analysis before the sequence is deposited in a database and described in a published article. Although describing individual genes and their products or functions is sufficient to consider this description as an annotation, the depth of analysis reported in literature for different genomes vary widely, with some reports including additional information that goes beyond a simple annotation.[5] Furthermore, due to the size and complexity of sequenced genomes, DNA annotation is not performed manually, but is instead automated by computational means. However, the conclusions drawn from the obtained results require manual expert analysis.[6]

DNA annotation is classified into two categories: structural annotation, which identifies and demarcates elements in a genome, and functional annotation, which assigns functions to these elements.[7] This is not the only way in which it has been categorized, as several alternatives, such as dimension-based[8] and level-based classifications,[3] have also been proposed.

  1. ^ Zheng S, Poczai P, Hyvönen J, Tang J, Amiryousefi A (2020). "Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes". Frontiers in Genetics. 11 (576124): 576124. doi:10.3389/fgene.2020.576124. PMC 7545089. PMID 33101394.
  2. ^ Dominguez Del Angel V, Hjerde E, Sterck L, Capella-Gutierrez S, Notredame C, Vinnere Pettersson O, et al. (5 February 2018). "Ten steps to get started in Genome Assembly and Annotation". F1000Research. 7 (148): 148. doi:10.12688/f1000research.13598.1. PMC 5850084. PMID 29568489.
  3. ^ a b Stein L (July 2001). "Genome annotation: from sequence to biology". Nature Reviews. Genetics. 2 (7): 493–503. doi:10.1038/35080529. PMID 11433356. S2CID 12044602.
  4. ^ Davis CP (29 March 2021). "Medical Definition of Genome annotation". MedicineNet. Archived from the original on 9 February 2023. Retrieved 17 April 2023.
  5. ^ Koonin E, Galperin MY (2003). "Genome Annotation and Analysis". Sequence — Evolution — Function (1st ed.). Springer US. pp. 193–226. doi:10.1007/978-1-4757-3783-7_6. ISBN 978-1-4757-3783-7.
  6. ^ Mishra P, Maurya R, Avashthi H, Mittal S, Chandra M, Ramteke PW (2021). "Genome assembly and annotation". In Singh DB, Pathak RK (eds.). Bioinformatics: Methods and Applications (1st ed.). Elsevier Science. pp. 49–66. doi:10.1016/B978-0-323-89775-4.00013-4. ISBN 9780323897754.
  7. ^ Bright LA, Burgess SC, Chowdhary B, Swiderski CE, McCarthy FM (October 2009). "Structural and functional-annotation of an equine whole genome oligoarray". BMC Bioinformatics. 10 (Suppl 11): S8. doi:10.1186/1471-2105-10-S11-S8. PMC 3226197. PMID 19811692.
  8. ^ Reed JL, Famili I, Thiele I, Palsson BO (February 2006). "Towards multidimensional genome annotation". Nature Reviews. Genetics. 7 (2): 130–141. doi:10.1038/nrg1769. PMID 16418748. S2CID 13107786.