Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder

We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended...

Full description

Saved in:

Bibliographic Details
Published in:	DNA research Vol. 16; no. 5; pp. 261 - 273
Main Authors:	Sharov, Alexei A., Ko, Minoru S.H.
Format:	Journal Article
Language:	English
Published:	Oxford Oxford University Press 01.10.2009
Subjects:	Algorithms Amino Acid Motifs Animals Base Sequence Binding Sites Biological and medical sciences Computational Biology - methods Embryonic Stem Cells - metabolism Fundamental and applied biological sciences. Psychology Genes. Genome Genetics of eukaryotes. Biological and molecular evolution Molecular and cellular biology Molecular genetics Pluripotent Stem Cells - metabolism Position-Specific Scoring Matrices Software Transcription Factors - metabolism ChIP-seq transcription factor binding site software embryonic stem cells algorithm Nucleotide sequence Embryonic cell Stem cell Software Binding site Transcription factor Chip Algorithm
ISSN:	1340-2838, 1756-1663, 1756-1663
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Abstract	We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended over gaps and flanking regions and clustered to generate non-redundant sets of motifs. The algorithm successfully identified binding motifs for 12 transcription factors (TFs) in embryonic stem cells based on published chromatin immunoprecipitation sequencing data. Furthermore, CisFinder successfully identified alternative binding motifs of TFs (e.g. POU5F1, ESRRB, and CTCF) and motifs for known and unknown co-factors of genes associated with the pluripotent state of ES cells. CisFinder also showed robust performance in the identification of motifs that were only slightly enriched in a set of DNA sequences.
AbstractList	We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended over gaps and flanking regions and clustered to generate non-redundant sets of motifs. The algorithm successfully identified binding motifs for 12 transcription factors (TFs) in embryonic stem cells based on published chromatin immunoprecipitation sequencing data. Furthermore, CisFinder successfully identified alternative binding motifs of TFs (e.g. POU5F1, ESRRB, and CTCF) and motifs for known and unknown co-factors of genes associated with the pluripotent state of ES cells. CisFinder also showed robust performance in the identification of motifs that were only slightly enriched in a set of DNA sequences.We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended over gaps and flanking regions and clustered to generate non-redundant sets of motifs. The algorithm successfully identified binding motifs for 12 transcription factors (TFs) in embryonic stem cells based on published chromatin immunoprecipitation sequencing data. Furthermore, CisFinder successfully identified alternative binding motifs of TFs (e.g. POU5F1, ESRRB, and CTCF) and motifs for known and unknown co-factors of genes associated with the pluripotent state of ES cells. CisFinder also showed robust performance in the identification of motifs that were only slightly enriched in a set of DNA sequences. We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended over gaps and flanking regions and clustered to generate non-redundant sets of motifs. The algorithm successfully identified binding motifs for 12 transcription factors (TFs) in embryonic stem cells based on published chromatin immunoprecipitation sequencing data. Furthermore, CisFinder successfully identified alternative binding motifs of TFs (e.g. POU5F1, ESRRB, and CTCF) and motifs for known and unknown co-factors of genes associated with the pluripotent state of ES cells. CisFinder also showed robust performance in the identification of motifs that were only slightly enriched in a set of DNA sequences.
Author	Sharov, Alexei A. Ko, Minoru S.H.
AuthorAffiliation	Developmental Genomics and Aging Section, Laboratory of Genetics , National Institute on Aging, NIH , Baltimore, MD 21224 , USA
AuthorAffiliation_xml	– name: Developmental Genomics and Aging Section, Laboratory of Genetics , National Institute on Aging, NIH , Baltimore, MD 21224 , USA
Author_xml	– sequence: 1 givenname: Alexei A. surname: Sharov fullname: Sharov, Alexei A. organization: National Institute on Aging, NIH – sequence: 2 givenname: Minoru S.H. surname: Ko fullname: Ko, Minoru S.H. email: kom@mail.nih.gov organization: National Institute on Aging, NIH
BackLink	http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=22037539$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/19740934$$D View this record in MEDLINE/PubMed
BookMark	eNqNkstv1DAQxi3UirYLR64oFx6XUD_j5IJULS1UKvQAnC3HGbNGWTu1kwX-exxlKQWJx8mW5jfffPM4QQc-eEDoEcEvCG7Yaed1hHTapQETfg8dEymqklQVO8h_xnFJa1YfoZOUPmPMiWDyPjoijeQ5mR-jy_OvGz2l0e2geA86mk1hQyyudxDLCEOWBj9CV7x6d5bjNxN4A8XbMDqbii9u3BRrly6c7yA-QIdW9wke7t8V-nhx_mH9pry6fn25PrsqjSBkLEVTt4KCMdhoC40lVjRdy-uOcmDcat3YtiICm4qKhkgjWt2ZBixpMsutYCv0ctEdpnYLncn-ou7VEN1Wx28qaKd-jXi3UZ_CTlFZ0bnrFXq2F4ghN5RGtXXJQN9rD2FKSuap1ZWoZvLpX0lKeMXx_4FcSkIy-Piu-VvXPxaSgSd7QCejexu1Ny7dcpRiJgWbK5YLZ2JIKYL9KYXVfBhqOQy1HEbm2W-8caMeXZhn5Po_Zj1fssI0_KPAd9dtzcg
CitedBy_id	crossref_primary_10_1016_j_stem_2009_07_012 crossref_primary_10_1093_hmg_ddt553 crossref_primary_10_1186_1745_6150_9_4 crossref_primary_10_1093_nar_gkaa368 crossref_primary_10_1093_nar_gks389 crossref_primary_10_1016_j_ymeth_2014_08_006 crossref_primary_10_1371_journal_pone_0067156 crossref_primary_10_1101_gr_101469_109 crossref_primary_10_1016_j_stem_2013_09_003 crossref_primary_10_1038_nature11171 crossref_primary_10_1101_gr_125666_111 crossref_primary_10_1186_s12864_018_4630_0 crossref_primary_10_1101_gad_627811 crossref_primary_10_1007_s10577_023_09738_4 crossref_primary_10_1186_1471_2164_12_637 crossref_primary_10_1182_blood_2016_08_733469 crossref_primary_10_1016_j_ymthe_2023_01_002 crossref_primary_10_1186_1471_2105_11_551 crossref_primary_10_1182_blood_2013_12_543801 crossref_primary_10_1371_journal_pone_0078179 crossref_primary_10_1073_pnas_1019537108 crossref_primary_10_1186_1471_2164_16_S7_S13 crossref_primary_10_1016_j_exphem_2011_05_008 crossref_primary_10_1089_cmb_2017_0100 crossref_primary_10_1016_j_patrec_2011_05_002 crossref_primary_10_1371_journal_pgen_1002770 crossref_primary_10_1042_BCJ20170418 crossref_primary_10_1093_nargab_lqab026 crossref_primary_10_1089_cmb_2012_0233 crossref_primary_10_1093_bib_bbaa229 crossref_primary_10_1371_journal_pone_0086044 crossref_primary_10_1371_journal_pgen_1005001 crossref_primary_10_1371_journal_pone_0016432 crossref_primary_10_1155_2016_4986707 crossref_primary_10_1109_TCBB_2015_2511750 crossref_primary_10_1038_nature09531 crossref_primary_10_1007_s12652_020_02013_y crossref_primary_10_1073_pnas_2008013117 crossref_primary_10_1186_1471_2105_13_176 crossref_primary_10_1038_nprot_2014_083 crossref_primary_10_1016_j_bbagrm_2013_10_001 crossref_primary_10_1016_j_compbiolchem_2016_01_014 crossref_primary_10_1093_bib_bbs016 crossref_primary_10_1109_TCBB_2022_3158471 crossref_primary_10_1093_bib_bbab070 crossref_primary_10_2174_1573394714666180417161728 crossref_primary_10_1186_1741_7007_8_128 crossref_primary_10_15252_msb_20167131 crossref_primary_10_1261_rna_035667_112 crossref_primary_10_1093_bib_bbab233 crossref_primary_10_1186_1471_2105_14_227 crossref_primary_10_1109_TCBB_2016_2609918 crossref_primary_10_1186_1471_2164_12_102 crossref_primary_10_1038_s41598_017_16009_w crossref_primary_10_1089_cmb_2016_0080 crossref_primary_10_15252_embr_201540467 crossref_primary_10_1038_nature12287 crossref_primary_10_1093_bioinformatics_btq546 crossref_primary_10_1038_ncomms4904 crossref_primary_10_1038_s41389_018_0108_9 crossref_primary_10_1093_bib_bbx026 crossref_primary_10_1093_nargab_lqae090 crossref_primary_10_3390_ijms25021011 crossref_primary_10_1007_s00018_018_2748_5 crossref_primary_10_1101_gad_348174_120 crossref_primary_10_3389_fcell_2021_642697 crossref_primary_10_7554_eLife_12717 crossref_primary_10_1155_2015_218068 crossref_primary_10_1101_gad_176008_111 crossref_primary_10_1371_journal_pone_0048102 crossref_primary_10_1016_j_compbiolchem_2016_02_003 crossref_primary_10_1093_nar_gku1261 crossref_primary_10_1158_1541_7786_MCR_11_0488 crossref_primary_10_1007_s11517_021_02468_x crossref_primary_10_1109_TNB_2015_2421340 crossref_primary_10_1186_1471_2164_15_678 crossref_primary_10_1002_stem_1279 crossref_primary_10_1101_gr_121541_111 crossref_primary_10_1089_cmb_2017_0005 crossref_primary_10_1182_blood_2016_05_714493 crossref_primary_10_1186_s12575_018_0088_3 crossref_primary_10_3390_e21080802 crossref_primary_10_1093_bib_bbq060 crossref_primary_10_1371_journal_pgen_1003728
Cites_doi	10.1101/gr.072769.107 10.1016/j.cell.2008.04.043 10.1101/gr.072942.107 10.1093/nar/gkm235 10.1002/j.1460-2075.1989.tb08393.x 10.1038/nmeth1068 10.1093/bioinformatics/btl147 10.1016/S0092-8674(00)00189-6 10.1093/dnares/dsl005 10.1093/nar/gkg585 10.1186/1475-4924-2-11 10.1093/nar/gkg108 10.1101/gr.080663.108 10.1038/sj.embor.7400334 10.1126/science.1162327 10.1093/nar/gkl198 10.1093/jb/mvm231 10.1186/1471-2105-8-193 10.1093/nar/18.20.6097 10.1073/pnas.0701811104 10.1101/gad.9.21.2635 10.1038/nature03441 10.1093/bioinformatics/btm546 10.1093/nar/gkg129 10.1038/nbt1053 10.1186/1471-2164-8-96 10.1038/ng1760 10.1006/jmbi.1998.1947 10.1186/1471-2164-8-365 10.1073/pnas.95.25.14863 10.1093/nar/gkg608 10.1371/journal.pcbi.1000010 10.1186/1471-2105-8-46 10.1101/gad.12.13.2073 10.1016/j.bioeng.2007.06.001 10.1016/j.cell.2007.05.009 10.1128/MCB.24.11.4791-4800.2004 10.1093/nar/gkn361 10.1186/gb-2007-8-2-r24 10.1186/1471-2105-7-280 10.1093/biostatistics/kxm058 10.1093/nar/23.23.4878 10.1093/nar/gkm955 10.1016/S0092-8674(00)81967-4 10.1038/nbt717 10.1016/j.cell.2008.05.024 10.1016/j.ygeno.2008.09.013 10.1126/science.1141319
ContentType	Journal Article
Copyright	The Author 2009. Published by Oxford University Press on behalf of Kazusa DNA Research Institute 2009 2009 INIST-CNRS The Author 2009. Published by Oxford University Press on behalf of Kazusa DNA Research Institute
Copyright_xml	– notice: The Author 2009. Published by Oxford University Press on behalf of Kazusa DNA Research Institute 2009 – notice: 2009 INIST-CNRS – notice: The Author 2009. Published by Oxford University Press on behalf of Kazusa DNA Research Institute
DBID	AAYXX CITATION IQODW CGR CUY CVF ECM EIF NPM 7TM 7X8 5PM
DOI	10.1093/dnares/dsp014
DatabaseName	CrossRef Pascal-Francis Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed Nucleic Acids Abstracts MEDLINE - Academic PubMed Central (Full Participant titles)
DatabaseTitle	CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) Nucleic Acids Abstracts MEDLINE - Academic
DatabaseTitleList	MEDLINE - Academic MEDLINE Nucleic Acids Abstracts Nucleic Acids Abstracts
Database_xml	– sequence: 1 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: 7X8 name: MEDLINE - Academic url: https://search.proquest.com/medline sourceTypes: Aggregation Database
DeliveryMethod	fulltext_linktorsrc
Discipline	Biology
EISSN	1756-1663
EndPage	273
ExternalDocumentID	PMC2762409 19740934 22037539 10_1093_dnares_dsp014 10.1093/dnares/dsp014
Genre	Journal Article Research Support, N.I.H., Intramural
GrantInformation_xml	– fundername: Intramural NIH HHS
GroupedDBID	--- .I3 0R~ 18M 1TH 29G 2WC 4.4 53G 5GY 5VS 5WA 70E AAFWJ AAHBH AAMVS AAOGV AAPPN AAPXW AAVAP ABPTD ABQLI ABQTQ ABSAR ABSMQ ABXVV ACFRR ACGFO ACGFS ACUTJ ADBBV ADHZD ADRAZ AEGXH AENEX AENZO AFPKN AFULF AGMDO AIAGR ALMA_UNASSIGNED_HOLDINGS ALUQC AOIJS ASAOO ATDFG BAWUL BAYMD BCNDV BTTYL C1A CIDKT CS3 CXTWN CZ4 DFGAJ DIK DU5 D~K E3Z EBD EBS EJD EMOBN F5P GROUPED_DOAJ GX1 H13 HH5 HYE HZ~ KQ8 KSI M48 MBTAY M~E O5R O5S OAWHX OJQWA OK1 O~Y P2P PEELM RD5 RNS ROX ROZ RPM RXO SV3 TOX TR2 WG7 X7H ZKX ~91 ~D7 ~S- AAYXX ABEJV ABGNP ACVCV AMNDL CITATION OVT APJGH IQODW CGR CUY CVF ECM EIF NPM 7TM 7X8 5PM
ID	FETCH-LOGICAL-c511t-598b52ecc0cafe9f1f59db48d24e34faa9fb6150c625917c5badc9ef199f14f53
IEDL.DBID	TOX
ISICitedReferencesCount	101
ISICitedReferencesURI	http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000271610400002&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
ISSN	1340-2838 1756-1663
IngestDate	Tue Sep 30 16:45:36 EDT 2025 Fri Jul 11 13:25:56 EDT 2025 Fri Jul 11 07:36:57 EDT 2025 Thu Jul 10 19:02:49 EDT 2025 Mon Jul 21 05:59:21 EDT 2025 Mon Jul 21 09:16:55 EDT 2025 Tue Nov 18 21:53:05 EST 2025 Sat Nov 29 04:41:39 EST 2025 Wed Aug 28 03:24:23 EDT 2024
IsDoiOpenAccess	true
IsOpenAccess	true
IsPeerReviewed	true
IsScholarly	true
Issue	5
Keywords	ChIP-seq transcription factor binding site software embryonic stem cells algorithm Nucleotide sequence Embryonic cell Stem cell Software Binding site Transcription factor Chip Algorithm
Language	English
License	CC BY 4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
LinkModel	DirectLink
MergedId	FETCHMERGED-LOGICAL-c511t-598b52ecc0cafe9f1f59db48d24e34faa9fb6150c625917c5badc9ef199f14f53
Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
OpenAccessLink	http://dx.doi.org/10.1093/dnares/dsp014
PMID	19740934
PQID	21447711
PQPubID	23462
PageCount	13
ParticipantIDs	pubmedcentral_primary_oai_pubmedcentral_nih_gov_2762409 proquest_miscellaneous_734086569 proquest_miscellaneous_21464069 proquest_miscellaneous_21447711 pubmed_primary_19740934 pascalfrancis_primary_22037539 crossref_primary_10_1093_dnares_dsp014 crossref_citationtrail_10_1093_dnares_dsp014 oup_primary_10_1093_dnares_dsp014
PublicationCentury	2000
PublicationDate	2009-10-01
PublicationDateYYYYMMDD	2009-10-01
PublicationDate_xml	– month: 10 year: 2009 text: 2009-10-01 day: 01
PublicationDecade	2000
PublicationPlace	Oxford
PublicationPlace_xml	– name: Oxford – name: England
PublicationTitle	DNA research
PublicationTitleAlternate	DNA Res
PublicationYear	2009
Publisher	Oxford University Press
Publisher_xml	– name: Oxford University Press
References	(45_28383578) 2007; 104 (34_22596889) 2006; 13 Gupta (25_23704993) 2007; 8 (41_29920976) 2008; 143 Xie (46_18740820) 2005; 434 Kel (30_17690809) 2003; 31 Bailey (15_22356683) 2006; 34 Karolchik (35_17466483) 2003; 31 (7_31110052) 2008; 18 Berger (8_31404064) 2008; 133 Thompson (16_17690810) 2003; 31 (32_31647860) 2008; 18 Hess (22_28341572) 2007; 8 (23_24186043) 1995; 57 (48_28508504) 2007; 35 Robertson (5_29170702) 2007; 4 Zhang (52_18389439) 2003; 2 van Helden (26_6134355) 1998; 281 (4_28787857) 2007; 316 (39_30309924) 2008; 18 (18_30650550) 2008; 9 Sandve (13_28883145) 2007; 8 Bell (42_10935193) 1999; 98 Liu (20_17171480) 2002; 20 Scholer (50_5451853) 1989; 8 Yuan (40_16078587) 1995; 9 Eisen (27_6256485) 1998; 95 (12_32762039) 2007; 8 Quandt (31_16138936) 1995; 23 Kim (49_32403546) 2009; 93 (2_34846372) 2009; 324 Schneider (28_9220356) 1990; 18 Barski (3_28749794) 2007; 129 Matys (47_17466564) 2003; 31 Loh (10_21854008) 2006; 38 (19_31294203) 2008; 36 Szabo (44_18182384) 2004; 24 Moon (43_18659311) 2005; 6 Reiss (53_22228984) 2006; 7 Bruce (51_29612762) 2007; 8 (17_21967145) 2006; 22 Stoltenburg (1_29470382) 2007; 24 Pavesi (36_23636639) 2007; 8 Tompa (14_18607581) 2005; 23 Habib (24_31055028) 2008; 4 Lieb (6_17597485) 2003; 224 (11_29890081) 2008; 24 Botquin (38_6064387) 1998; 12 Tomilin (37_10587003) 2000; 103 Chen (9_31312085) 2008; 133 (33_29876407) 2008; 36 18212089 - Genome Res. 2008 Apr;18(4):631-9 16845028 - Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W369-73 17558387 - Nat Methods. 2007 Aug;4(8):651-7 12824369 - Nucleic Acids Res. 2003 Jul 1;31(13):3576-9 7590241 - Genes Dev. 1995 Nov 1;9(21):2635-45 16518401 - Nat Genet. 2006 Apr;38(4):431-40 15637633 - Nat Biotechnol. 2005 Jan;23(1):137-44 12101404 - Nat Biotechnol. 2002 Aug;20(8):835-9 8532532 - Nucleic Acids Res. 1995 Dec 11;23(23):4878-84 17419876 - BMC Genomics. 2007;8:96 12824370 - Nucleic Acids Res. 2003 Jul 1;31(13):3580-5 17512414 - Cell. 2007 May 18;129(4):823-37 18682548 - Genome Res. 2008 Nov;18(11):1752-62 2172928 - Nucleic Acids Res. 1990 Oct 25;18(20):6097-100 17324271 - Genome Biol. 2007;8(2):R24 17478514 - Nucleic Acids Res. 2007;35(10):3442-52 9649510 - Genes Dev. 1998 Jul 1;12(13):2073-90 15678159 - EMBO Rep. 2005 Feb;6(2):165-70 18555785 - Cell. 2008 Jun 13;133(6):1106-17 18349034 - Biostatistics. 2008 Oct;9(4):668-85 10458613 - Cell. 1999 Aug 6;98(3):387-96 18463706 - PLoS Comput Biol. 2008 Feb;4(2):e1000010 12814519 - J Biol. 2003;2(2):11 16980320 - DNA Res. 2006 Jun 30;13(3):123-34 17925037 - BMC Genomics. 2007;8:365 18950698 - Genomics. 2009 Feb;93(2):152-8 12519945 - Nucleic Acids Res. 2003 Jan 1;31(1):51-4 15143173 - Mol Cell Biol. 2004 Jun;24(11):4791-800 18556756 - Nucleic Acids Res. 2008 Jul;36(12):4137-48 18024971 - Bioinformatics. 2008 Jan 1;24(1):1-10 9719638 - J Mol Biol. 1998 Sep 4;281(5):827-42 16632495 - Bioinformatics. 2006 Jul 1;22(13):1577-84 18006571 - Nucleic Acids Res. 2008 Jan;36(Database issue):D102-6 11136971 - Cell. 2000 Dec 8;103(6):853-64 18047721 - BMC Bioinformatics. 2007;8 Suppl 7:S21 19443739 - Science. 2009 Jun 26;324(5935):1720-3 18490265 - Genome Res. 2008 Aug;18(8):1325-35 12710669 - Methods Mol Biol. 2003;224:99-109 9843981 - Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8 18585359 - Cell. 2008 Jun 27;133(7):1266-76 17540862 - Science. 2007 Jun 8;316(5830):1497-502 16749936 - BMC Bioinformatics. 2006;7:280 18039682 - J Biochem. 2008 Mar;143(3):395-406 15735639 - Nature. 2005 Mar 17;434(7031):338-45 17442748 - Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7145-50 17627883 - Biomol Eng. 2007 Oct;24(4):381-403 17559676 - BMC Bioinformatics. 2007;8:193 17286865 - BMC Bioinformatics. 2007;8:46 12520026 - Nucleic Acids Res. 2003 Jan 1;31(1):374-8 2573524 - EMBO J. 1989 Sep;8(9):2551-7
References_xml	– volume: 18 start-page: 1325 issn: 1088-9051 issue: 8 year: 2008 ident: 7_31110052 publication-title: Genome Research doi: 10.1101/gr.072769.107 – volume: 133 start-page: 1106 issn: 0092-8674 issue: 6 year: 2008 ident: 9_31312085 publication-title: Cell doi: 10.1016/j.cell.2008.04.043 – volume: 18 start-page: 631 issn: 1088-9051 issue: 4 year: 2008 ident: 39_30309924 publication-title: Genome Research doi: 10.1101/gr.072942.107 – volume: 35 start-page: 3442 issn: 0305-1048 issue: 10 year: 2007 ident: 48_28508504 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkm235 – volume: 8 start-page: 2551 issn: 0261-4189 issue: 9 year: 1989 ident: 50_5451853 publication-title: The EMBO Journal doi: 10.1002/j.1460-2075.1989.tb08393.x – volume: 4 start-page: 651 issn: 1548-7091 issue: 8 year: 2007 ident: 5_29170702 doi: 10.1038/nmeth1068 – volume: 22 start-page: 1577 issn: 1367-4803 issue: 13 year: 2006 ident: 17_21967145 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btl147 – volume: 103 start-page: 853 issn: 0092-8674 issue: 6 year: 2000 ident: 37_10587003 publication-title: Cell doi: 10.1016/S0092-8674(00)00189-6 – volume: 13 start-page: 123 issn: 1340-2838 issue: 3 year: 2006 ident: 34_22596889 publication-title: DNA Research doi: 10.1093/dnares/dsl005 – volume: 31 start-page: 3576 issn: 0305-1048 issue: 13 year: 2003 ident: 30_17690809 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkg585 – volume: 2 start-page: 11 issn: 1478-5854 issue: 2 year: 2003 ident: 52_18389439 publication-title: Journal of biology (Online) doi: 10.1186/1475-4924-2-11 – volume: 57 start-page: 289 year: 1995 ident: 23_24186043 publication-title: J R STAT SOC SER B – volume: 31 start-page: 374 issn: 0305-1048 issue: 1 year: 2003 ident: 47_17466564 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkg108 – volume: 18 start-page: 1752 issn: 1088-9051 issue: 11 year: 2008 ident: 32_31647860 publication-title: Genome Research doi: 10.1101/gr.080663.108 – volume: 6 start-page: 165 issn: 1469-221X issue: 2 year: 2005 ident: 43_18659311 publication-title: EMBO Reports doi: 10.1038/sj.embor.7400334 – volume: 324 start-page: 1720 issn: 0036-8075 issue: 5935 year: 2009 ident: 2_34846372 publication-title: Science doi: 10.1126/science.1162327 – volume: 34 start-page: W369 issn: 0305-1048 issue: Web Server year: 2006 ident: 15_22356683 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkl198 – volume: 143 start-page: 395 issn: 0021-924X issue: 3 year: 2008 ident: 41_29920976 publication-title: Journal of Biochemistry doi: 10.1093/jb/mvm231 – volume: 8 start-page: 193 issn: 1471-2105 year: 2007 ident: 13_28883145 publication-title: BMC bioinformatics [electronic resource] doi: 10.1186/1471-2105-8-193 – volume: 18 start-page: 6097 issn: 0305-1048 issue: 20 year: 1990 ident: 28_9220356 publication-title: Nucleic Acids Research doi: 10.1093/nar/18.20.6097 – volume: 104 start-page: 7145 issn: 0027-8424 issue: 17 year: 2007 ident: 45_28383578 publication-title: PNAS doi: 10.1073/pnas.0701811104 – volume: 9 start-page: 2635 issn: 0890-9369 issue: 21 year: 1995 ident: 40_16078587 publication-title: Genes & Development doi: 10.1101/gad.9.21.2635 – volume: 434 start-page: 338 issn: 1476-4687 issue: 7031 year: 2005 ident: 46_18740820 publication-title: Nature; Physical Science (London) doi: 10.1038/nature03441 – volume: 24 start-page: 1 issn: 1367-4803 issue: 1 year: 2008 ident: 11_29890081 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btm546 – volume: 31 start-page: 51 issn: 0305-1048 issue: 1 year: 2003 ident: 35_17466483 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkg129 – volume: 23 start-page: 137 issn: 1087-0156 issue: 1 year: 2005 ident: 14_18607581 publication-title: Nature biotechnology doi: 10.1038/nbt1053 – volume: 8 start-page: 96 issn: 1471-2164 year: 2007 ident: 22_28341572 publication-title: BMC genomics [electronic resource] doi: 10.1186/1471-2164-8-96 – volume: 38 start-page: 431 issn: 1061-4036 issue: 4 year: 2006 ident: 10_21854008 publication-title: Nature genetics doi: 10.1038/ng1760 – volume: 281 start-page: 827 issn: 0022-2836 issue: 5 year: 1998 ident: 26_6134355 publication-title: Journal of molecular biology doi: 10.1006/jmbi.1998.1947 – volume: 8 start-page: 365 issn: 1471-2164 year: 2007 ident: 51_29612762 publication-title: BMC genomics [electronic resource] doi: 10.1186/1471-2164-8-365 – volume: 8 start-page: S21 issn: 1471-2105 year: 2007 ident: 12_32762039 publication-title: BMC bioinformatics [electronic resource] – volume: 95 start-page: 14863 issn: 0027-8424 issue: 25 year: 1998 ident: 27_6256485 publication-title: PNAS doi: 10.1073/pnas.95.25.14863 – volume: 31 start-page: 3580 issn: 0305-1048 issue: 13 year: 2003 ident: 16_17690810 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkg608 – volume: 4 start-page: e1000010 issn: 1553-734X issue: 2 year: 2008 ident: 24_31055028 doi: 10.1371/journal.pcbi.1000010 – volume: 8 start-page: 46 issn: 1471-2105 year: 2007 ident: 36_23636639 publication-title: BMC bioinformatics [electronic resource] doi: 10.1186/1471-2105-8-46 – volume: 12 start-page: 2073 issn: 0890-9369 issue: 13 year: 1998 ident: 38_6064387 publication-title: Genes & Development doi: 10.1101/gad.12.13.2073 – volume: 24 start-page: 381 issn: 1389-0344 issue: 4 year: 2007 ident: 1_29470382 publication-title: Biomolecular engineering doi: 10.1016/j.bioeng.2007.06.001 – volume: 129 start-page: 823 issn: 0092-8674 issue: 4 year: 2007 ident: 3_28749794 publication-title: Cell doi: 10.1016/j.cell.2007.05.009 – volume: 24 start-page: 4791 issn: 0270-7306 issue: 11 year: 2004 ident: 44_18182384 publication-title: Molecular and Cellular Biology doi: 10.1128/MCB.24.11.4791-4800.2004 – volume: 224 start-page: 99 issn: 1064-3745 year: 2003 ident: 6_17597485 publication-title: Methods in molecular biology (Clifton, N.J.) – volume: 36 start-page: 4137 issn: 0305-1048 issue: 12 year: 2008 ident: 19_31294203 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkn361 – volume: 8 start-page: R24 issn: 1465-6906 issue: 2 year: 2007 ident: 25_23704993 publication-title: Genome biology doi: 10.1186/gb-2007-8-2-r24 – volume: 7 start-page: 280 issn: 1471-2105 year: 2006 ident: 53_22228984 publication-title: BMC bioinformatics [electronic resource] doi: 10.1186/1471-2105-7-280 – volume: 9 start-page: 668 issn: 1465-4644 issue: 4 year: 2008 ident: 18_30650550 publication-title: Biostatistics doi: 10.1093/biostatistics/kxm058 – volume: 23 start-page: 4878 issn: 0305-1048 issue: 23 year: 1995 ident: 31_16138936 publication-title: Nucleic Acids Research doi: 10.1093/nar/23.23.4878 – volume: 36 start-page: D102 issn: 0305-1048 issue: suppl_1 year: 2008 ident: 33_29876407 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkm955 – volume: 98 start-page: 387 issn: 0092-8674 issue: 3 year: 1999 ident: 42_10935193 publication-title: Cell doi: 10.1016/S0092-8674(00)81967-4 – volume: 20 start-page: 835 issn: 1087-0156 issue: 8 year: 2002 ident: 20_17171480 publication-title: Nature biotechnology doi: 10.1038/nbt717 – volume: 133 start-page: 1266 issn: 0092-8674 issue: 7 year: 2008 ident: 8_31404064 publication-title: Cell doi: 10.1016/j.cell.2008.05.024 – volume: 93 start-page: 152 issn: 0888-7543 issue: 2 year: 2009 ident: 49_32403546 publication-title: Genomics doi: 10.1016/j.ygeno.2008.09.013 – volume: 316 start-page: 1497 issn: 0036-8075 issue: 5830 year: 2007 ident: 4_28787857 publication-title: Science doi: 10.1126/science.1141319 – reference: 15143173 - Mol Cell Biol. 2004 Jun;24(11):4791-800 – reference: 12814519 - J Biol. 2003;2(2):11 – reference: 18212089 - Genome Res. 2008 Apr;18(4):631-9 – reference: 17478514 - Nucleic Acids Res. 2007;35(10):3442-52 – reference: 8532532 - Nucleic Acids Res. 1995 Dec 11;23(23):4878-84 – reference: 17286865 - BMC Bioinformatics. 2007;8:46 – reference: 17442748 - Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7145-50 – reference: 18490265 - Genome Res. 2008 Aug;18(8):1325-35 – reference: 18585359 - Cell. 2008 Jun 27;133(7):1266-76 – reference: 18463706 - PLoS Comput Biol. 2008 Feb;4(2):e1000010 – reference: 16845028 - Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W369-73 – reference: 18039682 - J Biochem. 2008 Mar;143(3):395-406 – reference: 12101404 - Nat Biotechnol. 2002 Aug;20(8):835-9 – reference: 12824370 - Nucleic Acids Res. 2003 Jul 1;31(13):3580-5 – reference: 9649510 - Genes Dev. 1998 Jul 1;12(13):2073-90 – reference: 17558387 - Nat Methods. 2007 Aug;4(8):651-7 – reference: 15678159 - EMBO Rep. 2005 Feb;6(2):165-70 – reference: 16518401 - Nat Genet. 2006 Apr;38(4):431-40 – reference: 17419876 - BMC Genomics. 2007;8:96 – reference: 17540862 - Science. 2007 Jun 8;316(5830):1497-502 – reference: 17627883 - Biomol Eng. 2007 Oct;24(4):381-403 – reference: 2573524 - EMBO J. 1989 Sep;8(9):2551-7 – reference: 17324271 - Genome Biol. 2007;8(2):R24 – reference: 17925037 - BMC Genomics. 2007;8:365 – reference: 18950698 - Genomics. 2009 Feb;93(2):152-8 – reference: 11136971 - Cell. 2000 Dec 8;103(6):853-64 – reference: 18349034 - Biostatistics. 2008 Oct;9(4):668-85 – reference: 12710669 - Methods Mol Biol. 2003;224:99-109 – reference: 18682548 - Genome Res. 2008 Nov;18(11):1752-62 – reference: 18555785 - Cell. 2008 Jun 13;133(6):1106-17 – reference: 7590241 - Genes Dev. 1995 Nov 1;9(21):2635-45 – reference: 12519945 - Nucleic Acids Res. 2003 Jan 1;31(1):51-4 – reference: 2172928 - Nucleic Acids Res. 1990 Oct 25;18(20):6097-100 – reference: 16632495 - Bioinformatics. 2006 Jul 1;22(13):1577-84 – reference: 16749936 - BMC Bioinformatics. 2006;7:280 – reference: 15637633 - Nat Biotechnol. 2005 Jan;23(1):137-44 – reference: 18006571 - Nucleic Acids Res. 2008 Jan;36(Database issue):D102-6 – reference: 16980320 - DNA Res. 2006 Jun 30;13(3):123-34 – reference: 12824369 - Nucleic Acids Res. 2003 Jul 1;31(13):3576-9 – reference: 15735639 - Nature. 2005 Mar 17;434(7031):338-45 – reference: 9843981 - Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8 – reference: 19443739 - Science. 2009 Jun 26;324(5935):1720-3 – reference: 10458613 - Cell. 1999 Aug 6;98(3):387-96 – reference: 9719638 - J Mol Biol. 1998 Sep 4;281(5):827-42 – reference: 17512414 - Cell. 2007 May 18;129(4):823-37 – reference: 12520026 - Nucleic Acids Res. 2003 Jan 1;31(1):374-8 – reference: 17559676 - BMC Bioinformatics. 2007;8:193 – reference: 18047721 - BMC Bioinformatics. 2007;8 Suppl 7:S21 – reference: 18024971 - Bioinformatics. 2008 Jan 1;24(1):1-10 – reference: 18556756 - Nucleic Acids Res. 2008 Jul;36(12):4137-48
SSID	ssj0041537
Score	2.2698345
Snippet	We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency...
SourceID	pubmedcentral proquest pubmed pascalfrancis crossref oup
SourceType	Open Access Repository Aggregation Database Index Database Enrichment Source Publisher
StartPage	261
SubjectTerms	Algorithms Amino Acid Motifs Animals Base Sequence Binding Sites Biological and medical sciences Computational Biology - methods Embryonic Stem Cells - metabolism Fundamental and applied biological sciences. Psychology Genes. Genome Genetics of eukaryotes. Biological and molecular evolution Molecular and cellular biology Molecular genetics Pluripotent Stem Cells - metabolism Position-Specific Scoring Matrices Software Transcription Factors - metabolism
Title	Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder
URI	https://www.ncbi.nlm.nih.gov/pubmed/19740934 https://www.proquest.com/docview/21447711 https://www.proquest.com/docview/21464069 https://www.proquest.com/docview/734086569 https://pubmed.ncbi.nlm.nih.gov/PMC2762409
Volume	16
WOSCitedRecordID	wos000271610400002&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
hasFullText	1
inHoldings	1
isFullTextHit
isPrint
journalDatabaseRights	– providerCode: PRVAON databaseName: Directory of Open Access Journals customDbUrl: eissn: 1756-1663 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0041537 issn: 1340-2838 databaseCode: DOA dateStart: 19940101 isFulltext: true titleUrlDefault: https://www.doaj.org/ providerName: Directory of Open Access Journals – providerCode: PRVASL databaseName: Oxford Journals Open Access Collection customDbUrl: eissn: 1756-1663 dateEnd: 20121231 omitProxy: false ssIdentifier: ssj0041537 issn: 1340-2838 databaseCode: TOX dateStart: 19940101 isFulltext: true titleUrlDefault: https://academic.oup.com/journals/ providerName: Oxford University Press – providerCode: PRVASL databaseName: Oxford Journals Open Access Collection customDbUrl: eissn: 1756-1663 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0041537 issn: 1340-2838 databaseCode: TOX dateStart: 19960101 isFulltext: true titleUrlDefault: https://academic.oup.com/journals/ providerName: Oxford University Press
link	http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwjV1Rb9MwED6NaZOQJtgGbB2s8yTEE9HqxJ7tx6m0Agm6PRTUtyhxbLUSSqumneDfc7bTjm4t9NlfJOfu7Dvbd98BvOc5hsnoOKJYGBsxI3DNcc0iZjGYb0k8y_kK7x9fRa8nBwN1V993VGue8FVyVZSuEueqqCYt37GacukMun87WGy56IQ8OSZNWCtCfylrMs0nX684n1DQdjDJKpSGDW0s1sWZj9Ml__I_3Zfbz_wQXtQxJrkJRnEEO6Y8hv3QdfL3K_jS-TV0bD-4z5GQbUwwciW3aNSR57h09UimIJ96NzgeMq3Jt_FsZCvirm1Je1R1Hcvi9DV873b67c9R3VEh0hhYzSKuZM5j1FpLZ9YoSy1XRc5kETOTMJtlyuaOIV67UxEVmudZoZWxVCGWWZ68gd1yXJpTIJQVOuPMxYuGXedUasfbY0SB57uEJ6wBHxeiTnVNN-66XvxMw7N3kgbppEE6DfiwhE8Cz8Ym4CXq7X-Y5opWl-g4di1_E9WAi4WaU1xO7o0kK814XqWOQU4ISv-JuHblwg0gGxACzVBinIyQk2A5D9PF4xtOF2coVmxqCXBs36sj5WjoWb9jdFv47dkW__8WnvtHL59z-A52Z9O5OYc9fT8bVdMmPBMD2fSXD02_jP4Ar5AcMQ
linkProvider	Oxford University Press
openUrl	ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Exhaustive+Search+for+Over-represented+DNA+Sequence+Motifs+with+CisFinder&rft.jtitle=DNA+research&rft.au=Sharov%2C+A.+A.&rft.au=Ko%2C+M.+S.H.&rft.date=2009-10-01&rft.issn=1340-2838&rft.eissn=1756-1663&rft.volume=16&rft.issue=5&rft.spage=261&rft.epage=273&rft_id=info:doi/10.1093%2Fdnares%2Fdsp014&rft.externalDBID=n%2Fa&rft.externalDocID=10_1093_dnares_dsp014
thumbnail_l	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1340-2838&client=summon
thumbnail_m	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1340-2838&client=summon
thumbnail_s	http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1340-2838&client=summon