Editing Coding region (section)

== Coding sequence detection ==
[[File:Human karyotype with bands and sub-bands.png|thumb|Schematic [[karyotype|karyogram]] of a human, showing an overview of the [[human genome]] on [[G banding]] (which includes [[Giemsa-stain]]ing), wherein coding DNA regions occur to a greater extent in lighter ([[GC-content|GC rich]]) regions.<ref name=Romiguier2017>{{cite journal| author=Romiguier J, Roux C| title=Analytical Biases Associated with GC-Content in Molecular Evolution. | journal=Front Genet | year= 2017 | volume= 8 | issue=  | pages= 16 | pmid=28261263 | doi=10.3389/fgene.2017.00016 | pmc=5309256 | doi-access=free }} </ref><br>{{further|Karyotype}}]]
While identification of [[open reading frames]] within a DNA sequence is straightforward, identifying coding sequences is not, because the cell translates only a subset of all open reading frames to proteins.<ref>{{cite journal | vauthors = Furuno M, Kasukawa T, Saito R, Adachi J, Suzuki H, Baldarelli R, Hayashizaki Y, Okazaki Y | display-authors = 6 | title = CDS annotation in full-length cDNA sequence | journal = Genome Research | volume = 13 | issue = 6B | pages = 1478–87 | date = June 2003 | pmid = 12819146 | pmc = 403693 | doi = 10.1101/gr.1060303 | publisher = Cold Spring Harbor Laboratory Press }}</ref> Currently CDS prediction uses sampling and sequencing of mRNA from cells, although there is still the problem of determining which parts of a given mRNA are actually translated to protein. CDS prediction is a subset of [[gene prediction]], the latter also including prediction of DNA sequences that code not only for protein but also for other functional elements such as RNA genes and regulatory sequences.

In both [[prokaryote]]s and [[eukaryote]]s, [[Overlapping gene|gene overlapping]] occurs relatively often in both DNA and RNA viruses as an evolutionary advantage to reduce genome size while retaining the ability to produce various proteins from the available coding regions.<ref>{{cite journal | vauthors = Rogozin IB, Spiridonov AN, Sorokin AV, Wolf YI, Jordan IK, Tatusov RL, Koonin EV | title = Purifying and directional selection in overlapping prokaryotic genes | language = en | journal = Trends in Genetics | volume = 18 | issue = 5 | pages = 228–32 | date = May 2002 | pmid = 12047938 | doi = 10.1016/S0168-9525(02)02649-5 | url = https://www.cell.com/trends/genetics/abstract/S0168-9525(02)02649-5 | url-access = subscription }}</ref><ref>{{cite journal | vauthors = Chirico N, Vianelli A, Belshaw R | title = Why genes overlap in viruses | journal = Proceedings. Biological Sciences | volume = 277 | issue = 1701 | pages = 3809–17 | date = December 2010 | pmid = 20610432 | pmc = 2992710 | doi = 10.1098/rspb.2010.1052 }}</ref> For both DNA and RNA, [[Sequence alignment#Pairwise alignment|pairwise alignments]] can detect overlapping coding regions, including short [[open reading frame]]s in viruses, but would require a known coding strand to compare the potential overlapping coding strand with.<ref>{{cite journal | vauthors = Firth AE, Brown CM | title = Detecting overlapping coding sequences with pairwise alignments | journal = Bioinformatics | volume = 21 | issue = 3 | pages = 282–92 | date = February 2005 | pmid = 15347574 | doi = 10.1093/bioinformatics/bti007 | url = https://academic.oup.com/bioinformatics/article/21/3/282/237775 | doi-access = free }}</ref> An alternative method using single genome sequences would not require multiple genome sequences to execute comparisons but would require at least 50 nucleotides overlapping in order to be sensitive.<ref>{{cite journal | vauthors = Schlub TE, Buchmann JP, Holmes EC | title = A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences | journal = Molecular Biology and Evolution | volume = 35 | issue = 10 | pages = 2572–2581 | date = October 2018 | pmid = 30099499 | pmc = 6188560 | doi = 10.1093/molbev/msy155 | editor-first = Harmit | editor-last = Malik }}</ref>