Editing Nucleic acid sequence (section)

=== Sequence alignment ===
{{Main|Sequence alignment}}

In bioinformatics, a sequence alignment is a way of arranging the sequences of [[DNA]], [[RNA]], or [[protein]] to identify regions of similarity that may be due to functional, [[structural biology|structural]], or [[evolution]]ary relationships between the sequences.<ref name="mount">{{Cite book |last=Mount DM. |title=Bioinformatics: Sequence and Genome Analysis |publisher=Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY |year=2004 |isbn=0-87969-608-7 |edition=2nd}}</ref> If two sequences in an alignment share a common ancestor, mismatches can be interpreted as [[point mutation]]s and gaps as [[Insertion (genetics)|insertion]] or [[Deletion (genetics)|deletion mutations]] ([[indel]]s) introduced in one or both lineages in the time since they diverged from one another. In sequence alignments of proteins, the degree of similarity between [[amino acid]]s occupying a particular position in the sequence can be interpreted as a rough measure of how [[conservation (genetics)|conserved]] a particular region or [[sequence motif]] is among lineages. The absence of substitutions, or the presence of only very conservative substitutions (that is, the substitution of amino acids whose [[side chain]]s have similar biochemical properties) in a particular region of the sequence, suggest<ref name="predict">{{Cite journal |last=Ng |first=P. C. |last2=Henikoff |first2=S. |year=2001 |title=Predicting Deleterious Amino Acid Substitutions |journal=Genome Research |volume=11 |issue=5 |pages=863–74 |doi=10.1101/gr.176601 |pmc=311071 |pmid=11337480}}</ref> that this region has structural or functional importance. Although DNA and RNA [[nucleotide]] bases are more similar to each other than are amino acids, the conservation of base pairs can indicate a similar functional or structural role.<ref>{{Cite journal |last=Witzany |first=G |year=2016 |title=Crucial steps to life: From chemical reactions to code using agents |url=https://philpapers.org/rec/GUECST-2 |journal=Biosystems |volume=140 |pages=49–57 |bibcode=2016BiSys.140...49W |doi=10.1016/j.biosystems.2015.12.007 |pmid=26723230 |s2cid=30962295}}</ref>

[[Computational phylogenetics]] makes extensive use of sequence alignments in the construction and interpretation of [[phylogenetic tree]]s, which are used to classify the evolutionary relationships between homologous genes represented in the genomes of divergent species. The degree to which sequences in a query set differ is qualitatively related to the sequences' evolutionary distance from one another. Roughly speaking, high sequence identity suggests that the sequences in question have a comparatively young [[most recent common ancestor]], while low identity suggests that the divergence is more ancient. This approximation, which reflects the "[[molecular clock]]" hypothesis that a roughly constant [[rate of evolution|rate of evolutionary change]] can be used to extrapolate the elapsed time since two genes first diverged (that is, the [[coalescence (genetics)|coalescence]] time), assumes that the effects of mutation and [[natural selection|selection]] are constant across sequence lineages. Therefore, it does not account for possible differences among organisms or species in the rates of [[DNA repair]] or the possible functional conservation of specific regions in a sequence. (In the case of nucleotide sequences, the molecular clock hypothesis in its most basic form also discounts the difference in acceptance rates between [[silent mutation]]s that do not alter the meaning of a given [[codon]] and other mutations that result in a different [[amino acid]] being incorporated into the protein.) More statistically accurate methods allow the evolutionary rate on each branch of the phylogenetic tree to vary, thus producing better estimates of coalescence times for genes.