WordCluster: detecting clusters of DNA words and genomic elements
Identifieur interne : 000802 ( Ncbi/Merge ); précédent : 000801; suivant : 000803WordCluster: detecting clusters of DNA words and genomic elements
Auteurs : Michael Hackenberg [Espagne] ; Pedro Carpena [Espagne, États-Unis] ; Pedro Bernaola-Galván [Espagne] ; Guillermo Barturen [Espagne] ; Ángel M. Alganza [Espagne] ; José L. Oliver [Espagne]Source :
- Algorithms for Molecular Biology : AMB [ 1748-7188 ] ; 2011.
Abstract
Many
We introduce here an algorithm to detect clusters of DNA words (
Url:
DOI: 10.1186/1748-7188-6-2
PubMed: 21261981
PubMed Central: 3037320
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wicri:stream="Checkpoint" wicri:step="PubMed">001D25</idno><idno type="wicri:Area/Ncbi/Merge">000802</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>WordCluster</italic>: detecting clusters of DNA words and genomic elements</title><author><name sortKey="Hackenberg, Michael" sort="Hackenberg, Michael" uniqKey="Hackenberg M" first="Michael" last="Hackenberg">Michael Hackenberg</name><affiliation wicri:level="4"><nlm:aff id="I1">Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author><author><name sortKey="Carpena, Pedro" sort="Carpena, Pedro" uniqKey="Carpena P" first="Pedro" last="Carpena">Pedro Carpena</name><affiliation wicri:level="2"><nlm:aff id="I2">Dpto. de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga 29071-Malaga, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga 29071-Malaga</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Division of Sleep Medicine, Brigham and Woman's Hospital, Harvard Medical School, Boston, MA 02115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Sleep Medicine, Brigham and Woman's Hospital, Harvard Medical School, Boston, MA 02115</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Bernaola Galvan, Pedro" sort="Bernaola Galvan, Pedro" uniqKey="Bernaola Galvan P" first="Pedro" last="Bernaola-Galván">Pedro Bernaola-Galván</name><affiliation wicri:level="2"><nlm:aff id="I2">Dpto. de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga 29071-Malaga, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga 29071-Malaga</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region></placeName></affiliation></author><author><name sortKey="Barturen, Guillermo" sort="Barturen, Guillermo" uniqKey="Barturen G" first="Guillermo" last="Barturen">Guillermo Barturen</name><affiliation wicri:level="4"><nlm:aff id="I1">Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author><author><name sortKey="Alganza, Angel M" sort="Alganza, Angel M" uniqKey="Alganza A" first="Ángel M" last="Alganza">Ángel M. Alganza</name><affiliation wicri:level="4"><nlm:aff id="I1">Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author><author><name sortKey="Oliver, Jose L" sort="Oliver, Jose L" uniqKey="Oliver J" first="José L" last="Oliver">José L. Oliver</name><affiliation wicri:level="4"><nlm:aff id="I1">Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author></analytic><series><title level="j">Algorithms for Molecular Biology : AMB</title><idno type="eISSN">1748-7188</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Many <italic>k-</italic>mers (or DNA words) and genomic elements are known to be spatially clustered in the genome. Well established examples are the genes, TFBSs, CpG dinucleotides, microRNA genes and ultra-conserved non-coding regions. Currently, no algorithm exists to find these clusters in a statistically comprehensible way. The detection of clustering often relies on densities and sliding-window approaches or arbitrarily chosen distance thresholds.</p></sec><sec><title>Results</title><p>We introduce here an algorithm to detect clusters of DNA words (<italic>k-</italic>mers), or any other genomic element, based on the distance between consecutive copies and an assigned statistical significance. We implemented the method into a web server connected to a MySQL backend, which also determines the co-localization with gene annotations. We demonstrate the usefulness of this approach by detecting the clusters of CAG/CTG (cytosine contexts that can be methylated in undifferentiated cells), showing that the degree of methylation vary drastically between inside and outside of the clusters. As another example, we used <italic>WordCluster </italic>to search for statistically significant clusters of olfactory receptor (OR) genes in the human genome.</p></sec><sec><title>Conclusions</title><p><italic>WordCluster </italic>seems to predict biological meaningful clusters of DNA words (<italic>k-</italic>mers) and genomic entities. The implementation of the method into a web server is available at <ext-link ext-link-type="uri" xlink:href="http://bioinfo2.ugr.es/wordCluster/wordCluster.php">http://bioinfo2.ugr.es/wordCluster/wordCluster.php</ext-link> including additional features like the detection of co-localization with gene regions or the annotation enrichment tool for functional analysis of overlapped genes.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Durand, D" uniqKey="Durand D">D Durand</name></author><author><name sortKey="Sankoff, D" uniqKey="Sankoff D">D Sankoff</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gardiner Garden, M" uniqKey="Gardiner Garden M">M Gardiner-Garden</name></author><author><name sortKey="Frommer, M" uniqKey="Frommer M">M Frommer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Makeev, Vj" uniqKey="Makeev V">VJ Makeev</name></author><author><name sortKey="Lifanov, Ap" uniqKey="Lifanov A">AP Lifanov</name></author><author><name sortKey="Nazina, Ag" uniqKey="Nazina A">AG Nazina</name></author><author><name sortKey="Papatsenko, Da" uniqKey="Papatsenko D">DA Papatsenko</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sandelin, A" uniqKey="Sandelin A">A Sandelin</name></author><author><name sortKey="Bailey, P" uniqKey="Bailey P">P Bailey</name></author><author><name sortKey="Bruce, S" uniqKey="Bruce S">S Bruce</name></author><author><name sortKey="Engstrom, Pg" uniqKey="Engstrom P">PG Engstrom</name></author><author><name sortKey="Klos, Jm" uniqKey="Klos J">JM Klos</name></author><author><name sortKey="Wasserman, Ww" uniqKey="Wasserman W">WW Wasserman</name></author><author><name sortKey="Ericson, J" uniqKey="Ericson J">J Ericson</name></author><author><name sortKey="Lenhard, B" uniqKey="Lenhard B">B Lenhard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Carpena, P" uniqKey="Carpena P">P Carpena</name></author><author><name sortKey="Bernaola Galvan, P" uniqKey="Bernaola Galvan P">P Bernaola-Galván</name></author><author><name sortKey="Hackenberg, M" uniqKey="Hackenberg M">M Hackenberg</name></author><author><name sortKey="Coronado, Av" uniqKey="Coronado A">AV Coronado</name></author><author><name sortKey="Oliver, Jl" uniqKey="Oliver J">JL Oliver</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Giardine, B" uniqKey="Giardine B">B Giardine</name></author><author><name sortKey="Riemer, C" uniqKey="Riemer C">C Riemer</name></author><author><name sortKey="Hardison, Rc" uniqKey="Hardison R">RC Hardison</name></author><author><name sortKey="Burhans, R" uniqKey="Burhans R">R Burhans</name></author><author><name sortKey="Elnitski, L" uniqKey="Elnitski L">L Elnitski</name></author><author><name sortKey="Shah, P" uniqKey="Shah P">P Shah</name></author><author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y Zhang</name></author><author><name sortKey="Blankenberg, D" uniqKey="Blankenberg D">D Blankenberg</name></author><author><name sortKey="Albert, I" uniqKey="Albert I">I Albert</name></author><author><name sortKey="Taylor, J" uniqKey="Taylor J">J Taylor</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hackenberg, M" uniqKey="Hackenberg M">M Hackenberg</name></author><author><name sortKey="Previti, C" uniqKey="Previti C">C Previti</name></author><author><name sortKey="Luque Escamilla, Pl" uniqKey="Luque Escamilla P">PL Luque-Escamilla</name></author><author><name sortKey="Carpena, P" uniqKey="Carpena P">P Carpena</name></author><author><name sortKey="Martinez Aroza, J" uniqKey="Martinez Aroza J">J Martínez-Aroza</name></author><author><name sortKey="Oliver, Jl" uniqKey="Oliver J">JL Oliver</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Karolchik, D" uniqKey="Karolchik D">D Karolchik</name></author><author><name sortKey="Kuhn, Rm" uniqKey="Kuhn R">RM Kuhn</name></author><author><name sortKey="Baertsch, R" uniqKey="Baertsch R">R Baertsch</name></author><author><name sortKey="Barber, Gp" uniqKey="Barber G">GP Barber</name></author><author><name sortKey="Clawson, H" uniqKey="Clawson H">H Clawson</name></author><author><name sortKey="Diekhans, M" uniqKey="Diekhans M">M Diekhans</name></author><author><name sortKey="Giardine, B" uniqKey="Giardine B">B Giardine</name></author><author><name sortKey="Harte, Ra" uniqKey="Harte R">RA Harte</name></author><author><name sortKey="Hinrichs, As" uniqKey="Hinrichs A">AS Hinrichs</name></author><author><name sortKey="Hsu, F" uniqKey="Hsu F">F Hsu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Quinlan, Ar" uniqKey="Quinlan A">AR Quinlan</name></author><author><name sortKey="Hall, Im" uniqKey="Hall I">IM Hall</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ashburner, M" uniqKey="Ashburner M">M Ashburner</name></author><author><name sortKey="Ball, Ca" uniqKey="Ball C">CA Ball</name></author><author><name sortKey="Blake, Ja" uniqKey="Blake J">JA Blake</name></author><author><name sortKey="Botstein, D" uniqKey="Botstein D">D Botstein</name></author><author><name sortKey="Butler, H" uniqKey="Butler H">H Butler</name></author><author><name sortKey="Cherry, Jm" uniqKey="Cherry J">JM Cherry</name></author><author><name sortKey="Davis, Ap" uniqKey="Davis A">AP Davis</name></author><author><name sortKey="Dolinski, K" uniqKey="Dolinski K">K Dolinski</name></author><author><name sortKey="Dwight, Ss" uniqKey="Dwight S">SS Dwight</name></author><author><name sortKey="Eppig, Jt" uniqKey="Eppig J">JT Eppig</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hackenberg, M" uniqKey="Hackenberg M">M Hackenberg</name></author><author><name sortKey="Matthiesen, R" uniqKey="Matthiesen R">R Matthiesen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hackenberg, M" uniqKey="Hackenberg M">M Hackenberg</name></author><author><name sortKey="Matthiesen, R" uniqKey="Matthiesen R">R Matthiesen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pruitt, Kd" uniqKey="Pruitt K">KD Pruitt</name></author><author><name sortKey="Tatusova, T" uniqKey="Tatusova T">T Tatusova</name></author><author><name sortKey="Maglott, Dr" uniqKey="Maglott D">DR Maglott</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hubbard, Tj" uniqKey="Hubbard T">TJ Hubbard</name></author><author><name sortKey="Aken, Bl" uniqKey="Aken B">BL Aken</name></author><author><name sortKey="Ayling, S" uniqKey="Ayling S">S Ayling</name></author><author><name sortKey="Ballester, B" uniqKey="Ballester B">B Ballester</name></author><author><name sortKey="Beal, K" uniqKey="Beal K">K Beal</name></author><author><name sortKey="Bragin, E" uniqKey="Bragin E">E Bragin</name></author><author><name sortKey="Brent, S" uniqKey="Brent S">S Brent</name></author><author><name sortKey="Chen, Y" uniqKey="Chen Y">Y Chen</name></author><author><name sortKey="Clapham, P" uniqKey="Clapham P">P Clapham</name></author><author><name sortKey="Clarke, L" uniqKey="Clarke L">L Clarke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hackenberg, M" uniqKey="Hackenberg M">M Hackenberg</name></author><author><name sortKey="Barturen, G" uniqKey="Barturen G">G Barturen</name></author><author><name sortKey="Carpena, P" uniqKey="Carpena P">P Carpena</name></author><author><name sortKey="Luque Escamilla, Pl" uniqKey="Luque Escamilla P">PL Luque-Escamilla</name></author><author><name sortKey="Previti, C" uniqKey="Previti C">C Previti</name></author><author><name sortKey="Oliver, Jl" uniqKey="Oliver J">JL Oliver</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Siepel, A" uniqKey="Siepel A">A Siepel</name></author><author><name sortKey="Bejerano, G" uniqKey="Bejerano G">G Bejerano</name></author><author><name sortKey="Pedersen, Js" uniqKey="Pedersen J">JS Pedersen</name></author><author><name sortKey="Hinrichs, As" uniqKey="Hinrichs A">AS Hinrichs</name></author><author><name sortKey="Hou, M" uniqKey="Hou M">M Hou</name></author><author><name sortKey="Rosenbloom, K" uniqKey="Rosenbloom K">K Rosenbloom</name></author><author><name sortKey="Clawson, H" uniqKey="Clawson H">H Clawson</name></author><author><name sortKey="Spieth, J" uniqKey="Spieth J">J Spieth</name></author><author><name sortKey="Hillier, Lw" uniqKey="Hillier L">LW Hillier</name></author><author><name sortKey="Richards, S" uniqKey="Richards S">S Richards</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lister, R" uniqKey="Lister R">R Lister</name></author><author><name sortKey="Pelizzola, M" uniqKey="Pelizzola M">M Pelizzola</name></author><author><name sortKey="Dowen, Rh" uniqKey="Dowen R">RH Dowen</name></author><author><name sortKey="Hawkins, Rd" uniqKey="Hawkins R">RD Hawkins</name></author><author><name sortKey="Hon, G" uniqKey="Hon G">G Hon</name></author><author><name sortKey="Tonti Filippini, J" uniqKey="Tonti Filippini J">J Tonti-Filippini</name></author><author><name sortKey="Nery, Jr" uniqKey="Nery J">JR Nery</name></author><author><name sortKey="Lee, L" uniqKey="Lee L">L Lee</name></author><author><name sortKey="Ye, Z" uniqKey="Ye Z">Z Ye</name></author><author><name sortKey="Ngo, Qm" uniqKey="Ngo Q">QM Ngo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Aloni, R" uniqKey="Aloni R">R Aloni</name></author><author><name sortKey="Olender, T" uniqKey="Olender T">T Olender</name></author><author><name sortKey="Lancet, D" uniqKey="Lancet D">D Lancet</name></author></analytic></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><double pmid="21261981"><pmc><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en"><italic>WordCluster</italic>: detecting clusters of DNA words and genomic elements</title><author><name sortKey="Hackenberg, Michael" sort="Hackenberg, Michael" uniqKey="Hackenberg M" first="Michael" last="Hackenberg">Michael Hackenberg</name><affiliation wicri:level="4"><nlm:aff id="I1">Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author><author><name sortKey="Carpena, Pedro" sort="Carpena, Pedro" uniqKey="Carpena P" first="Pedro" last="Carpena">Pedro Carpena</name><affiliation wicri:level="2"><nlm:aff id="I2">Dpto. de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga 29071-Malaga, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga 29071-Malaga</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Division of Sleep Medicine, Brigham and Woman's Hospital, Harvard Medical School, Boston, MA 02115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Sleep Medicine, Brigham and Woman's Hospital, Harvard Medical School, Boston, MA 02115</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Bernaola Galvan, Pedro" sort="Bernaola Galvan, Pedro" uniqKey="Bernaola Galvan P" first="Pedro" last="Bernaola-Galván">Pedro Bernaola-Galván</name><affiliation wicri:level="2"><nlm:aff id="I2">Dpto. de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga 29071-Malaga, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga 29071-Malaga</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region></placeName></affiliation></author><author><name sortKey="Barturen, Guillermo" sort="Barturen, Guillermo" uniqKey="Barturen G" first="Guillermo" last="Barturen">Guillermo Barturen</name><affiliation wicri:level="4"><nlm:aff id="I1">Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author><author><name sortKey="Alganza, Angel M" sort="Alganza, Angel M" uniqKey="Alganza A" first="Ángel M" last="Alganza">Ángel M. Alganza</name><affiliation wicri:level="4"><nlm:aff id="I1">Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author><author><name sortKey="Oliver, Jose L" sort="Oliver, Jose L" uniqKey="Oliver J" first="José L" last="Oliver">José L. Oliver</name><affiliation wicri:level="4"><nlm:aff id="I1">Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21261981</idno><idno type="pmc">3037320</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037320</idno><idno type="RBID">PMC:3037320</idno><idno type="doi">10.1186/1748-7188-6-2</idno><date when="2011">2011</date><idno type="wicri:Area/Pmc/Corpus">000A32</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000A32</idno><idno type="wicri:Area/Pmc/Curation">000A32</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000A32</idno><idno type="wicri:Area/Pmc/Checkpoint">001340</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001340</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>WordCluster</italic>: detecting clusters of DNA words and genomic elements</title><author><name sortKey="Hackenberg, Michael" sort="Hackenberg, Michael" uniqKey="Hackenberg M" first="Michael" last="Hackenberg">Michael Hackenberg</name><affiliation wicri:level="4"><nlm:aff id="I1">Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author><author><name sortKey="Carpena, Pedro" sort="Carpena, Pedro" uniqKey="Carpena P" first="Pedro" last="Carpena">Pedro Carpena</name><affiliation wicri:level="2"><nlm:aff id="I2">Dpto. de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga 29071-Malaga, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga 29071-Malaga</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Division of Sleep Medicine, Brigham and Woman's Hospital, Harvard Medical School, Boston, MA 02115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Sleep Medicine, Brigham and Woman's Hospital, Harvard Medical School, Boston, MA 02115</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Bernaola Galvan, Pedro" sort="Bernaola Galvan, Pedro" uniqKey="Bernaola Galvan P" first="Pedro" last="Bernaola-Galván">Pedro Bernaola-Galván</name><affiliation wicri:level="2"><nlm:aff id="I2">Dpto. de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga 29071-Malaga, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga 29071-Malaga</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region></placeName></affiliation></author><author><name sortKey="Barturen, Guillermo" sort="Barturen, Guillermo" uniqKey="Barturen G" first="Guillermo" last="Barturen">Guillermo Barturen</name><affiliation wicri:level="4"><nlm:aff id="I1">Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author><author><name sortKey="Alganza, Angel M" sort="Alganza, Angel M" uniqKey="Alganza A" first="Ángel M" last="Alganza">Ángel M. Alganza</name><affiliation wicri:level="4"><nlm:aff id="I1">Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author><author><name sortKey="Oliver, Jose L" sort="Oliver, Jose L" uniqKey="Oliver J" first="José L" last="Oliver">José L. Oliver</name><affiliation wicri:level="4"><nlm:aff id="I1">Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author></analytic><series><title level="j">Algorithms for Molecular Biology : AMB</title><idno type="eISSN">1748-7188</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Many <italic>k-</italic>mers (or DNA words) and genomic elements are known to be spatially clustered in the genome. Well established examples are the genes, TFBSs, CpG dinucleotides, microRNA genes and ultra-conserved non-coding regions. Currently, no algorithm exists to find these clusters in a statistically comprehensible way. The detection of clustering often relies on densities and sliding-window approaches or arbitrarily chosen distance thresholds.</p></sec><sec><title>Results</title><p>We introduce here an algorithm to detect clusters of DNA words (<italic>k-</italic>mers), or any other genomic element, based on the distance between consecutive copies and an assigned statistical significance. We implemented the method into a web server connected to a MySQL backend, which also determines the co-localization with gene annotations. We demonstrate the usefulness of this approach by detecting the clusters of CAG/CTG (cytosine contexts that can be methylated in undifferentiated cells), showing that the degree of methylation vary drastically between inside and outside of the clusters. As another example, we used <italic>WordCluster </italic>to search for statistically significant clusters of olfactory receptor (OR) genes in the human genome.</p></sec><sec><title>Conclusions</title><p><italic>WordCluster </italic>seems to predict biological meaningful clusters of DNA words (<italic>k-</italic>mers) and genomic entities. The implementation of the method into a web server is available at <ext-link ext-link-type="uri" xlink:href="http://bioinfo2.ugr.es/wordCluster/wordCluster.php">http://bioinfo2.ugr.es/wordCluster/wordCluster.php</ext-link> including additional features like the detection of co-localization with gene regions or the annotation enrichment tool for functional analysis of overlapped genes.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Durand, D" uniqKey="Durand D">D Durand</name></author><author><name sortKey="Sankoff, D" uniqKey="Sankoff D">D Sankoff</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gardiner Garden, M" uniqKey="Gardiner Garden M">M Gardiner-Garden</name></author><author><name sortKey="Frommer, M" uniqKey="Frommer M">M Frommer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Makeev, Vj" uniqKey="Makeev V">VJ Makeev</name></author><author><name sortKey="Lifanov, Ap" uniqKey="Lifanov A">AP Lifanov</name></author><author><name sortKey="Nazina, Ag" uniqKey="Nazina A">AG Nazina</name></author><author><name sortKey="Papatsenko, Da" uniqKey="Papatsenko D">DA Papatsenko</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sandelin, A" uniqKey="Sandelin A">A Sandelin</name></author><author><name sortKey="Bailey, P" uniqKey="Bailey P">P Bailey</name></author><author><name sortKey="Bruce, S" uniqKey="Bruce S">S Bruce</name></author><author><name sortKey="Engstrom, Pg" uniqKey="Engstrom P">PG Engstrom</name></author><author><name sortKey="Klos, Jm" uniqKey="Klos J">JM Klos</name></author><author><name sortKey="Wasserman, Ww" uniqKey="Wasserman W">WW Wasserman</name></author><author><name sortKey="Ericson, J" uniqKey="Ericson J">J Ericson</name></author><author><name sortKey="Lenhard, B" uniqKey="Lenhard B">B Lenhard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Carpena, P" uniqKey="Carpena P">P Carpena</name></author><author><name sortKey="Bernaola Galvan, P" uniqKey="Bernaola Galvan P">P Bernaola-Galván</name></author><author><name sortKey="Hackenberg, M" uniqKey="Hackenberg M">M Hackenberg</name></author><author><name sortKey="Coronado, Av" uniqKey="Coronado A">AV Coronado</name></author><author><name sortKey="Oliver, Jl" uniqKey="Oliver J">JL Oliver</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Giardine, B" uniqKey="Giardine B">B Giardine</name></author><author><name sortKey="Riemer, C" uniqKey="Riemer C">C Riemer</name></author><author><name sortKey="Hardison, Rc" uniqKey="Hardison R">RC Hardison</name></author><author><name sortKey="Burhans, R" uniqKey="Burhans R">R Burhans</name></author><author><name sortKey="Elnitski, L" uniqKey="Elnitski L">L Elnitski</name></author><author><name sortKey="Shah, P" uniqKey="Shah P">P Shah</name></author><author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y Zhang</name></author><author><name sortKey="Blankenberg, D" uniqKey="Blankenberg D">D Blankenberg</name></author><author><name sortKey="Albert, I" uniqKey="Albert I">I Albert</name></author><author><name sortKey="Taylor, J" uniqKey="Taylor J">J Taylor</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hackenberg, M" uniqKey="Hackenberg M">M Hackenberg</name></author><author><name sortKey="Previti, C" uniqKey="Previti C">C Previti</name></author><author><name sortKey="Luque Escamilla, Pl" uniqKey="Luque Escamilla P">PL Luque-Escamilla</name></author><author><name sortKey="Carpena, P" uniqKey="Carpena P">P Carpena</name></author><author><name sortKey="Martinez Aroza, J" uniqKey="Martinez Aroza J">J Martínez-Aroza</name></author><author><name sortKey="Oliver, Jl" uniqKey="Oliver J">JL Oliver</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Karolchik, D" uniqKey="Karolchik D">D Karolchik</name></author><author><name sortKey="Kuhn, Rm" uniqKey="Kuhn R">RM Kuhn</name></author><author><name sortKey="Baertsch, R" uniqKey="Baertsch R">R Baertsch</name></author><author><name sortKey="Barber, Gp" uniqKey="Barber G">GP Barber</name></author><author><name sortKey="Clawson, H" uniqKey="Clawson H">H Clawson</name></author><author><name sortKey="Diekhans, M" uniqKey="Diekhans M">M Diekhans</name></author><author><name sortKey="Giardine, B" uniqKey="Giardine B">B Giardine</name></author><author><name sortKey="Harte, Ra" uniqKey="Harte R">RA Harte</name></author><author><name sortKey="Hinrichs, As" uniqKey="Hinrichs A">AS Hinrichs</name></author><author><name sortKey="Hsu, F" uniqKey="Hsu F">F Hsu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Quinlan, Ar" uniqKey="Quinlan A">AR Quinlan</name></author><author><name sortKey="Hall, Im" uniqKey="Hall I">IM Hall</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ashburner, M" uniqKey="Ashburner M">M Ashburner</name></author><author><name sortKey="Ball, Ca" uniqKey="Ball C">CA Ball</name></author><author><name sortKey="Blake, Ja" uniqKey="Blake J">JA Blake</name></author><author><name sortKey="Botstein, D" uniqKey="Botstein D">D Botstein</name></author><author><name sortKey="Butler, H" uniqKey="Butler H">H Butler</name></author><author><name sortKey="Cherry, Jm" uniqKey="Cherry J">JM Cherry</name></author><author><name sortKey="Davis, Ap" uniqKey="Davis A">AP Davis</name></author><author><name sortKey="Dolinski, K" uniqKey="Dolinski K">K Dolinski</name></author><author><name sortKey="Dwight, Ss" uniqKey="Dwight S">SS Dwight</name></author><author><name sortKey="Eppig, Jt" uniqKey="Eppig J">JT Eppig</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hackenberg, M" uniqKey="Hackenberg M">M Hackenberg</name></author><author><name sortKey="Matthiesen, R" uniqKey="Matthiesen R">R Matthiesen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hackenberg, M" uniqKey="Hackenberg M">M Hackenberg</name></author><author><name sortKey="Matthiesen, R" uniqKey="Matthiesen R">R Matthiesen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pruitt, Kd" uniqKey="Pruitt K">KD Pruitt</name></author><author><name sortKey="Tatusova, T" uniqKey="Tatusova T">T Tatusova</name></author><author><name sortKey="Maglott, Dr" uniqKey="Maglott D">DR Maglott</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hubbard, Tj" uniqKey="Hubbard T">TJ Hubbard</name></author><author><name sortKey="Aken, Bl" uniqKey="Aken B">BL Aken</name></author><author><name sortKey="Ayling, S" uniqKey="Ayling S">S Ayling</name></author><author><name sortKey="Ballester, B" uniqKey="Ballester B">B Ballester</name></author><author><name sortKey="Beal, K" uniqKey="Beal K">K Beal</name></author><author><name sortKey="Bragin, E" uniqKey="Bragin E">E Bragin</name></author><author><name sortKey="Brent, S" uniqKey="Brent S">S Brent</name></author><author><name sortKey="Chen, Y" uniqKey="Chen Y">Y Chen</name></author><author><name sortKey="Clapham, P" uniqKey="Clapham P">P Clapham</name></author><author><name sortKey="Clarke, L" uniqKey="Clarke L">L Clarke</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hackenberg, M" uniqKey="Hackenberg M">M Hackenberg</name></author><author><name sortKey="Barturen, G" uniqKey="Barturen G">G Barturen</name></author><author><name sortKey="Carpena, P" uniqKey="Carpena P">P Carpena</name></author><author><name sortKey="Luque Escamilla, Pl" uniqKey="Luque Escamilla P">PL Luque-Escamilla</name></author><author><name sortKey="Previti, C" uniqKey="Previti C">C Previti</name></author><author><name sortKey="Oliver, Jl" uniqKey="Oliver J">JL Oliver</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Siepel, A" uniqKey="Siepel A">A Siepel</name></author><author><name sortKey="Bejerano, G" uniqKey="Bejerano G">G Bejerano</name></author><author><name sortKey="Pedersen, Js" uniqKey="Pedersen J">JS Pedersen</name></author><author><name sortKey="Hinrichs, As" uniqKey="Hinrichs A">AS Hinrichs</name></author><author><name sortKey="Hou, M" uniqKey="Hou M">M Hou</name></author><author><name sortKey="Rosenbloom, K" uniqKey="Rosenbloom K">K Rosenbloom</name></author><author><name sortKey="Clawson, H" uniqKey="Clawson H">H Clawson</name></author><author><name sortKey="Spieth, J" uniqKey="Spieth J">J Spieth</name></author><author><name sortKey="Hillier, Lw" uniqKey="Hillier L">LW Hillier</name></author><author><name sortKey="Richards, S" uniqKey="Richards S">S Richards</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lister, R" uniqKey="Lister R">R Lister</name></author><author><name sortKey="Pelizzola, M" uniqKey="Pelizzola M">M Pelizzola</name></author><author><name sortKey="Dowen, Rh" uniqKey="Dowen R">RH Dowen</name></author><author><name sortKey="Hawkins, Rd" uniqKey="Hawkins R">RD Hawkins</name></author><author><name sortKey="Hon, G" uniqKey="Hon G">G Hon</name></author><author><name sortKey="Tonti Filippini, J" uniqKey="Tonti Filippini J">J Tonti-Filippini</name></author><author><name sortKey="Nery, Jr" uniqKey="Nery J">JR Nery</name></author><author><name sortKey="Lee, L" uniqKey="Lee L">L Lee</name></author><author><name sortKey="Ye, Z" uniqKey="Ye Z">Z Ye</name></author><author><name sortKey="Ngo, Qm" uniqKey="Ngo Q">QM Ngo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Aloni, R" uniqKey="Aloni R">R Aloni</name></author><author><name sortKey="Olender, T" uniqKey="Olender T">T Olender</name></author><author><name sortKey="Lancet, D" uniqKey="Lancet D">D Lancet</name></author></analytic></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI></pmc><pubmed><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">WordCluster: detecting clusters of DNA words and genomic elements.</title><author><name sortKey="Hackenberg, Michael" sort="Hackenberg, Michael" uniqKey="Hackenberg M" first="Michael" last="Hackenberg">Michael Hackenberg</name><affiliation wicri:level="4"><nlm:affiliation>Dpto, de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab, de Bioinformática, Centro de Investigación Biomédica, PTS, Avda, del Conocimiento s/n, 18100-Granada, Spain. mlhack@gmail.com.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto, de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab, de Bioinformática, Centro de Investigación Biomédica, PTS, Avda, del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author><author><name sortKey="Carpena, Pedro" sort="Carpena, Pedro" uniqKey="Carpena P" first="Pedro" last="Carpena">Pedro Carpena</name></author><author><name sortKey="Bernaola Galvan, Pedro" sort="Bernaola Galvan, Pedro" uniqKey="Bernaola Galvan P" first="Pedro" last="Bernaola-Galván">Pedro Bernaola-Galván</name></author><author><name sortKey="Barturen, Guillermo" sort="Barturen, Guillermo" uniqKey="Barturen G" first="Guillermo" last="Barturen">Guillermo Barturen</name></author><author><name sortKey="Alganza, Angel M" sort="Alganza, Angel M" uniqKey="Alganza A" first="Angel M" last="Alganza">Angel M. Alganza</name></author><author><name sortKey="Oliver, Jose L" sort="Oliver, Jose L" uniqKey="Oliver J" first="José L" last="Oliver">José L. Oliver</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2011">2011</date><idno type="RBID">pubmed:21261981</idno><idno type="pmid">21261981</idno><idno type="doi">10.1186/1748-7188-6-2</idno><idno type="wicri:Area/PubMed/Corpus">001F09</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001F09</idno><idno type="wicri:Area/PubMed/Curation">001F09</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001F09</idno><idno type="wicri:Area/PubMed/Checkpoint">001D25</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001D25</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">WordCluster: detecting clusters of DNA words and genomic elements.</title><author><name sortKey="Hackenberg, Michael" sort="Hackenberg, Michael" uniqKey="Hackenberg M" first="Michael" last="Hackenberg">Michael Hackenberg</name><affiliation wicri:level="4"><nlm:affiliation>Dpto, de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab, de Bioinformática, Centro de Investigación Biomédica, PTS, Avda, del Conocimiento s/n, 18100-Granada, Spain. mlhack@gmail.com.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto, de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab, de Bioinformática, Centro de Investigación Biomédica, PTS, Avda, del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author><author><name sortKey="Carpena, Pedro" sort="Carpena, Pedro" uniqKey="Carpena P" first="Pedro" last="Carpena">Pedro Carpena</name></author><author><name sortKey="Bernaola Galvan, Pedro" sort="Bernaola Galvan, Pedro" uniqKey="Bernaola Galvan P" first="Pedro" last="Bernaola-Galván">Pedro Bernaola-Galván</name></author><author><name sortKey="Barturen, Guillermo" sort="Barturen, Guillermo" uniqKey="Barturen G" first="Guillermo" last="Barturen">Guillermo Barturen</name></author><author><name sortKey="Alganza, Angel M" sort="Alganza, Angel M" uniqKey="Alganza A" first="Angel M" last="Alganza">Angel M. Alganza</name></author><author><name sortKey="Oliver, Jose L" sort="Oliver, Jose L" uniqKey="Oliver J" first="José L" last="Oliver">José L. Oliver</name></author></analytic><series><title level="j">Algorithms for molecular biology : AMB</title><idno type="eISSN">1748-7188</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Many k-mers (or DNA words) and genomic elements are known to be spatially clustered in the genome. Well established examples are the genes, TFBSs, CpG dinucleotides, microRNA genes and ultra-conserved non-coding regions. Currently, no algorithm exists to find these clusters in a statistically comprehensible way. The detection of clustering often relies on densities and sliding-window approaches or arbitrarily chosen distance thresholds.</div></front></TEI></pubmed></double></record>Pour manipuler ce document sous Unix (Dilib)
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