Editing Inverted repeat (section)

==Programs and databases==
The following list provides information and external links to various programs and databases for inverted repeats:
*[https://web.archive.org/web/20131113054733/http://nonb.abcc.ncifcrf.gov/apps/site/default non-B DB] A Database for Integrated Annotations and Analysis of non-B DNA Forming Motifs.<ref name=NONB>{{cite journal|last=Cer|first=RZ |author2=Donohue, DE |author3=Mudunuri, US |author4=Temiz, NA |author5=Loss, MA |author6=Starner, NJ |author7=Halusa, GN |author8=Volfovsky, N |author9=Yi, M |author10=Luke, BT |author11=Bacolla, A |author12=Collins, JR |author13=Stephens, RM|title=Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools|journal=Nucleic Acids Research|date=January 2013|volume=41|issue=Database issue|pages=D94–D100|pmid=23125372|doi=10.1093/nar/gks955|pmc=3531222}}</ref>  This database is provided by The Advanced Biomedical Computing Center (ABCC) at then Frederick National Laboratory for Cancer Research (FNLCR). It covers the [[A-DNA]] and [[Z-DNA]] conformations otherwise known as "non-B DNAs" because they are not the more [[B-DNA|common B-DNA]] form of a right-handed Watson-Crick [[nucleic acid double helix|double-helix]].  These "non-B DNAs" include left-handed Z-DNA, [[Cruciform#Cruciform DNA|cruciform]], [[triple-stranded DNA|triplex]], tetraplex and [[stem-loop|hairpin]] structures.<ref name=NONB /> Searches can be performed on a variety of "repeat types" (including inverted repeats) and on several species.
*[http://tandem.bu.edu/cgi-bin/irdb/irdb.exe Inverted Repeats Database] {{Webarchive|url=https://web.archive.org/web/20200901164938/http://tandem.bu.edu/cgi-bin/irdb/irdb.exe |date=2020-09-01 }} Boston University. This database is a web application that allows query and analysis of repeats held in the PUBLIC DATABASE project. Scientists can also analyze their own sequences with the Inverted Repeats Finder algorithm.<ref>{{cite journal|last=Gelfand|first=Y|author2=Rodriguez, A |author3=Benson, G |title=TRDB--the Tandem Repeats Database|journal=Nucleic Acids Research|date=January 2007|volume=35|issue=Database issue|pages=D80–7|pmid=17175540|doi=10.1093/nar/gkl1013|pmc=1781109}}</ref>
*[http://pmite.hzau.edu.cn/django/mite/ P-MITE: a Plant MITE database] &mdash;  this database for [[Miniature Inverted-repeat Transposable Elements]] (MITEs) contains sequences from [[Plant genomes#Plants|plant genomes]]. Sequences may be searched or downloaded from the database.<ref>{{cite journal|last=Chen|first=J|author2=Hu, Q |author3=Zhang, Y |author4=Lu, C |author5= Kuang, H |title=P-MITE: a database for plant miniature inverted-repeat transposable elements|journal=Nucleic Acids Research|date=Oct 29, 2013|pmid=24174541|doi=10.1093/nar/gkt1000|volume=42|issue=1|pages=D1176–81 |pmc=3964958}}</ref> 
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*[http://www.cbs.dtu.dk/services/GenomeAtlas/ Genome Atlas Database] — contains hundreds of examples
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*[[EMBOSS]] is the "European Molecular Biology Open Software Suite" which runs on [[UNIX]] and [[UNIX-like]] operating systems.<ref name=EMBOSS>{{cite journal|last=Rice|first=P|author2=Longden, I |author3=Bleasby, A |title=EMBOSS: the European Molecular Biology Open Software Suite|journal=Trends in Genetics|date=June 2000|volume=16|issue=6|pages=276–7|pmid=10827456|url=http://emboss.sourceforge.net/index.html|doi=10.1016/S0168-9525(00)02024-2|url-access=subscription}}</ref> Documentation and program source files are available on the [http://emboss.sourceforge.net/news/ EMBOSS website].  Applications specifically related to inverted repeats are listed below:
**[http://emboss.sourceforge.net/apps/cvs/emboss/apps/einverted.html EMBOSS einverted]: Finds inverted repeats in [[nucleic acid sequence|nucleotide sequences]]. Threshold values can be set to limit the scope of the search.<ref name=EMBOSS /> 
**[http://emboss.sourceforge.net/apps/cvs/emboss/apps/palindrome.html EMBOSS palindrome]: Finds [[palindromic sequence|palindromes]] such as [[stem-loop|stem loop]] regions in nucleotide sequences. The program will find sequences that include sections of mismatches and gaps that may correspond to bulges in a stem loop.<ref name=EMBOSS />