A fast algorithm for the construction of universal footprinting templates in DNA.
Identifieur interne : 000386 ( Ncbi/Checkpoint ); précédent : 000385; suivant : 000387A fast algorithm for the construction of universal footprinting templates in DNA.
Auteurs : James W. Anderson [Royaume-Uni] ; Keith R. Fox ; Graham A. NibloSource :
- Journal of mathematical biology [ 0303-6812 ] ; 2006.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA, Oligodeoxyribonucleotides.
- genetics : Base Pairing, DNA, Oligodeoxyribonucleotides.
- methods : DNA Footprinting.
- Algorithms, Sequence Analysis, DNA.
Abstract
We introduce and give a complete description of a new graph to be used for DNA sequencing questions. This graph has the advantage over the classical de Bruijn graph that it fully accounts for the double stranded nature of DNA, rather than dealing with single strands. Technically, our graph may be thought of as the quotient of the de Bruijn graph under the natural involution of sending a DNA strand to its complementary strand. However, this involution has fixed points, and this complicates the structure of the quotient graph which we have therefore modified herein. As an application and motivating example, we give an efficient algorithm for constructing universal footprinting templates for n-mers. This problem may be formulated as the task of finding a shortest possible segment of DNA which contains every possible sequence of base pairs of some fixed length n. Previous work by Kwan et al has attacked this problem from a numerical point of view and generated minimal length universal footprinting templates for n = 2, 3, 5, 7, together with unsubstantiated candidates for the case n = 4. We show that their candidates for n = 4 are indeed minimal length universal footprinting templates.
DOI: 10.1007/s00285-005-0357-z
PubMed: 16328479
Affiliations:
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Anderson</name><affiliation wicri:level="1"><nlm:affiliation>School of Mathematics, University of Southampton, Southampton, SO17 1BJ, United Kingdom. j.w.anderson@soton.ac.uk</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>School of Mathematics, University of Southampton, Southampton, SO17 1BJ</wicri:regionArea><wicri:noRegion>SO17 1BJ</wicri:noRegion></affiliation></author><author><name sortKey="Fox, Keith R" sort="Fox, Keith R" uniqKey="Fox K" first="Keith R" last="Fox">Keith R. Fox</name></author><author><name sortKey="Niblo, Graham A" sort="Niblo, Graham A" uniqKey="Niblo G" first="Graham A" last="Niblo">Graham A. Niblo</name></author></analytic><series><title level="j">Journal of mathematical biology</title><idno type="ISSN">0303-6812</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Base Pairing (genetics)</term><term>DNA (chemistry)</term><term>DNA (genetics)</term><term>DNA Footprinting (methods)</term><term>Oligodeoxyribonucleotides (chemistry)</term><term>Oligodeoxyribonucleotides (genetics)</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>ADN (génétique)</term><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Appariement de bases (génétique)</term><term>Oligodésoxyribonucléotides ()</term><term>Oligodésoxyribonucléotides (génétique)</term><term>Prise d'empreintes sur l'ADN ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term><term>Oligodeoxyribonucleotides</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Base Pairing</term><term>DNA</term><term>Oligodeoxyribonucleotides</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN</term><term>Appariement de bases</term><term>Oligodésoxyribonucléotides</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>DNA Footprinting</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Oligodésoxyribonucléotides</term><term>Prise d'empreintes sur l'ADN</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We introduce and give a complete description of a new graph to be used for DNA sequencing questions. This graph has the advantage over the classical de Bruijn graph that it fully accounts for the double stranded nature of DNA, rather than dealing with single strands. Technically, our graph may be thought of as the quotient of the de Bruijn graph under the natural involution of sending a DNA strand to its complementary strand. However, this involution has fixed points, and this complicates the structure of the quotient graph which we have therefore modified herein. As an application and motivating example, we give an efficient algorithm for constructing universal footprinting templates for n-mers. This problem may be formulated as the task of finding a shortest possible segment of DNA which contains every possible sequence of base pairs of some fixed length n. Previous work by Kwan et al has attacked this problem from a numerical point of view and generated minimal length universal footprinting templates for n = 2, 3, 5, 7, together with unsubstantiated candidates for the case n = 4. We show that their candidates for n = 4 are indeed minimal length universal footprinting templates.</div></front></TEI><affiliations><list><country><li>Royaume-Uni</li></country></list><tree><noCountry><name sortKey="Fox, Keith R" sort="Fox, Keith R" uniqKey="Fox K" first="Keith R" last="Fox">Keith R. Fox</name><name sortKey="Niblo, Graham A" sort="Niblo, Graham A" uniqKey="Niblo G" first="Graham A" last="Niblo">Graham A. Niblo</name></noCountry><country name="Royaume-Uni"><noRegion><name sortKey="Anderson, James W" sort="Anderson, James W" uniqKey="Anderson J" first="James W" last="Anderson">James W. Anderson</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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