Editing Nucleic acid sequence (section)

=== Notation ===
{{Main|Nucleic acid notation}}

While A, T, C, and G represent a particular nucleotide at a position, there are also letters that represent ambiguity which are used when more than one kind of nucleotide could occur at that position. The rules of the International Union of Pure and Applied Chemistry ([[IUPAC]]) are as follows:<ref name=":0">{{Cite journal |date=1986 |title=Nomenclature for incompletely specified bases in nucleic acid sequences. Recommendations 1984. Nomenclature Committee of the International Union of Biochemistry (NC-IUB). |journal=Proceedings of the National Academy of Sciences |language=en |volume=83 |issue=1 |pages=4–8 |doi=10.1073/pnas.83.1.4 |issn=0027-8424 |pmc=322779 |pmid=2417239 |doi-access=free}}</ref>

For example, '''W''' means that either an adenine or a thymine could occur in that position without impairing the sequence's functionality.

{| class="wikitable" style="margin-left:25px; margin-top:0px; text-align:center;"
|+List of symbols
! Symbol<ref name="iupac">{{Cite web |last=Nomenclature Committee of the International Union of Biochemistry (NC-IUB) |year=1984 |title=Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences |url=http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html |access-date=2008-02-04}}</ref> !! Meaning/derivation !!colspan=5| Possible bases|| Complement
|-
| '''A''' ||align=left| [[Adenine|'''A'''denine]] || A || || || ||rowspan=5| 1 || T (or U)
|-
| '''C''' ||align=left| [[Cytosine|'''C'''ytosine]] || || C || || || G
|-
| '''G''' ||align=left| [[Guanine|'''G'''uanine]] || || || G || || C
|-
| '''T''' ||align=left| [[Thymine|'''T'''hymine]] || || || || T  || A
|-
| '''U''' ||align=left| [[Uracil|'''U'''racil]] || || || || U || A
|- bgcolor=#e8e8e8
| '''W''' ||align=left| '''W'''eak || A || || || T ||rowspan=6| 2 || S
|- bgcolor=#e8e8e8
| '''S''' ||align=left| '''S'''trong || || C || G ||  || W
|- bgcolor=#e8e8e8
| '''M''' ||align=left| [[Amine|a'''M'''ino]] || A || C || || || K
|- bgcolor=#e8e8e8
| '''K''' ||align=left| [[Ketone|'''K'''eto]] || || || G || T  || M
|- bgcolor=#e8e8e8
| '''R''' ||align=left| [[Purine|pu'''R'''ine]] || A || || G ||  || Y
|- bgcolor=#e8e8e8
| '''Y''' ||align=left| [[Pyrimidine|p'''Y'''rimidine]] || || C || || T || R
|-
| '''B''' ||align=left|  not A ('''B''' comes after A) || || C || G || T  ||rowspan=4| 3 || V
|-
| '''D''' ||align=left|  not C ('''D''' comes after C) || A || || G || T || H
|-
| '''H''' ||align=left| not G ('''H''' comes after G)|| A || C || || T || D
|-
| '''V''' ||align=left| not T ('''V''' comes after T and U) || A || C || G || || B
|- bgcolor=#e8e8e8
| '''N''' ||align=left|  any '''N'''ucleotide (not a gap) || A || C || G || T || 4 || N
|-
|'''Z''' ||align=left| [[0|'''Z'''ero]] || || || ||  || 0 || Z
|}

These symbols are also valid for RNA, except with U (uracil) replacing T (thymine).<ref name=":0" />

Apart from adenine (A), cytosine (C), guanine (G), thymine (T) and uracil (U), DNA and RNA also contain bases that have been modified after the nucleic acid chain has been formed. In DNA, the most common modified base is [[5-Methylcytidine|5-methylcytidine]] (m5C). In RNA, there are many modified bases, including [[pseudouridine]] (Ψ), [[dihydrouridine]] (D), [[inosine]] (I), [[ribothymidine]] (rT) and [[7-methylguanosine]] (m7G).<ref>{{Cite web |title=BIOL2060: Translation |url=https://www.mun.ca/biology/desmid/brian/BIOL2060/BIOL2060-22/CB22.html |website=mun.ca}}</ref><ref>{{Cite web |title=Research |url=http://www.biogeo.uw.edu.pl/research/grupaC_en.html |website=uw.edu.pl}}</ref> [[Hypoxanthine]] and [[xanthine]] are two of the many bases created through [[mutagen]] presence, both of them through deamination (replacement of the amine-group with a carbonyl-group). Hypoxanthine is produced from [[adenine]], and xanthine is produced from [[guanine]].<ref>{{Cite journal |last=Nguyen |first=T |last2=Brunson |first2=D |last3=Crespi |first3=C L |last4=Penman |first4=B W |last5=Wishnok |first5=J S |last6=Tannenbaum |first6=S R |date=April 1992 |title=DNA damage and mutation in human cells exposed to nitric oxide in vitro |journal=Proc Natl Acad Sci USA |volume=89 |issue=7 |pages=3030–034 |bibcode=1992PNAS...89.3030N |doi=10.1073/pnas.89.7.3030 |pmc=48797 |pmid=1557408 |doi-access=free}}</ref> Similarly, deamination of [[cytosine]] results in [[uracil]].

;Example of comparing and determining the % difference between two nucleotide sequences
* AA'''T'''CC'''GC'''TAG
* AA'''A'''CC'''CT'''TAG

Given the two 10-nucleotide sequences, line them up and compare the differences between them. Calculate the percent difference by taking the number of differences between the DNA bases divided by the total number of nucleotides. In this case there are three differences in the 10 nucleotide sequence. Thus there is a 30% difference.