REMiner-II: A tool for rapid identification and configuration of repetitive element arrays from large mammalian chromosomes as a single query
Genes occupy ~3% of the human and mouse genomes whereas repetitive elements (REs), whose biologic functions are largely uncharacterized, constitute greater than 50%. A heterogeneous population of RE arrays (arrangement structures) is formed by combinations of various REs in mammalian genomes. In thi...
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| Veröffentlicht in: | Genomics (San Diego, Calif.) Calif.), 2012-09, Vol.100 (3), p.131-140 |
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| creator | Kim, Woo-Chan Lee, Kang-Hoon Shin, Kyung-Seop You, Ri-Na Lee, Young-Kwan Cho, Kiho Cho, Dong-Ho |
| description | Genes occupy ~3% of the human and mouse genomes whereas repetitive elements (REs), whose biologic functions are largely uncharacterized, constitute greater than 50%. A heterogeneous population of RE arrays (arrangement structures) is formed by combinations of various REs in mammalian genomes. In this study, REMiner-II was refined from the original REMiner for a more efficient identification and configuration of RE arrays from large queries (e.g., human chromosomes) using an unbiased self-alignment protocol. Chromosome-wide RE array profiles for the entire sets of human and mouse chromosomes were obtained using REMiner-II on a personal computer. REMiner-II provides 10 adjustable parameters and three data output modes to accommodate different experimental settings and/or goals. Examination of the human and mouse chromosome data using the REMiner-II viewer revealed species-specific libraries of complexly organized RE arrays. In conclusion, REMiner-II is an efficient tool for chromosome-wide identification and characterization of RE arrays from mammalian genomes. |
| doi_str_mv | 10.1016/j.ygeno.2012.06.006 |
| format | Article |
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A heterogeneous population of RE arrays (arrangement structures) is formed by combinations of various REs in mammalian genomes. In this study, REMiner-II was refined from the original REMiner for a more efficient identification and configuration of RE arrays from large queries (e.g., human chromosomes) using an unbiased self-alignment protocol. Chromosome-wide RE array profiles for the entire sets of human and mouse chromosomes were obtained using REMiner-II on a personal computer. REMiner-II provides 10 adjustable parameters and three data output modes to accommodate different experimental settings and/or goals. Examination of the human and mouse chromosome data using the REMiner-II viewer revealed species-specific libraries of complexly organized RE arrays. In conclusion, REMiner-II is an efficient tool for chromosome-wide identification and characterization of RE arrays from mammalian genomes.</description><identifier>ISSN: 0888-7543</identifier><identifier>EISSN: 1089-8646</identifier><identifier>DOI: 10.1016/j.ygeno.2012.06.006</identifier><identifier>PMID: 22750555</identifier><language>eng</language><publisher>Amsterdam: Elsevier Inc</publisher><subject>Algorithms ; Animals ; Biological and medical sciences ; Chromosome-wide ; chromosomes ; Chromosomes - genetics ; Computational Biology - methods ; Data Mining - methods ; Databases, Genetic ; Diverse techniques ; Fundamental and applied biological sciences. Psychology ; genes ; Genes. Genome ; Genetics of eukaryotes. Biological and molecular evolution ; Genome, Human ; Humans ; Internet ; Mammalian genome ; Mammals - genetics ; Mice ; Mining ; Molecular and cellular biology ; Molecular genetics ; Oligonucleotide Array Sequence Analysis - methods ; RE array ; REMiner-II ; Repetitive element ; Repetitive Sequences, Nucleic Acid ; Sequence Alignment - methods ; Software ; Species Specificity ; Time Factors</subject><ispartof>Genomics (San Diego, Calif.), 2012-09, Vol.100 (3), p.131-140</ispartof><rights>2012 Elsevier Inc.</rights><rights>2015 INIST-CNRS</rights><rights>Copyright © 2012 Elsevier Inc. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c491t-2e823f7e565cea88d0d2b3ae082fc946480e4c30d13f37135dca90f401a08adb3</citedby><cites>FETCH-LOGICAL-c491t-2e823f7e565cea88d0d2b3ae082fc946480e4c30d13f37135dca90f401a08adb3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.ygeno.2012.06.006$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=26340530$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22750555$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kim, Woo-Chan</creatorcontrib><creatorcontrib>Lee, Kang-Hoon</creatorcontrib><creatorcontrib>Shin, Kyung-Seop</creatorcontrib><creatorcontrib>You, Ri-Na</creatorcontrib><creatorcontrib>Lee, Young-Kwan</creatorcontrib><creatorcontrib>Cho, Kiho</creatorcontrib><creatorcontrib>Cho, Dong-Ho</creatorcontrib><title>REMiner-II: A tool for rapid identification and configuration of repetitive element arrays from large mammalian chromosomes as a single query</title><title>Genomics (San Diego, Calif.)</title><addtitle>Genomics</addtitle><description>Genes occupy ~3% of the human and mouse genomes whereas repetitive elements (REs), whose biologic functions are largely uncharacterized, constitute greater than 50%. A heterogeneous population of RE arrays (arrangement structures) is formed by combinations of various REs in mammalian genomes. In this study, REMiner-II was refined from the original REMiner for a more efficient identification and configuration of RE arrays from large queries (e.g., human chromosomes) using an unbiased self-alignment protocol. Chromosome-wide RE array profiles for the entire sets of human and mouse chromosomes were obtained using REMiner-II on a personal computer. REMiner-II provides 10 adjustable parameters and three data output modes to accommodate different experimental settings and/or goals. Examination of the human and mouse chromosome data using the REMiner-II viewer revealed species-specific libraries of complexly organized RE arrays. In conclusion, REMiner-II is an efficient tool for chromosome-wide identification and characterization of RE arrays from mammalian genomes.</description><subject>Algorithms</subject><subject>Animals</subject><subject>Biological and medical sciences</subject><subject>Chromosome-wide</subject><subject>chromosomes</subject><subject>Chromosomes - genetics</subject><subject>Computational Biology - methods</subject><subject>Data Mining - methods</subject><subject>Databases, Genetic</subject><subject>Diverse techniques</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>genes</subject><subject>Genes. Genome</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Genome, Human</subject><subject>Humans</subject><subject>Internet</subject><subject>Mammalian genome</subject><subject>Mammals - genetics</subject><subject>Mice</subject><subject>Mining</subject><subject>Molecular and cellular biology</subject><subject>Molecular genetics</subject><subject>Oligonucleotide Array Sequence Analysis - methods</subject><subject>RE array</subject><subject>REMiner-II</subject><subject>Repetitive element</subject><subject>Repetitive Sequences, Nucleic Acid</subject><subject>Sequence Alignment - methods</subject><subject>Software</subject><subject>Species Specificity</subject><subject>Time Factors</subject><issn>0888-7543</issn><issn>1089-8646</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkd-LEzEQxxdRvHr6FwiaF8GXrZNf26xwD8dxp4UTQb3nMM1Oasrupibbg_4R_s-m16pvCoGB4fPNDPOpqpcc5hx4824z369pjHMBXMyhmQM0j6oZB9PWplHN42oGxph6oZU8q57lvAGAVhrxtDoTYqFBaz2rfn65_hRGSvVy-Z5dsinGnvmYWMJt6FjoaJyCDw6nEEeGY8dcHH1Y79KxEz1LtKUpTOGeGPU0lADDlHCfmU9xYD2mNbEBhwH7gCNz30s35jhQZlgey2Fc98R-7Cjtn1dPPPaZXpzqeXV3c_3t6mN9-_nD8urytnaq5VMtyAjpF6Qb7QiN6aATK4kERnjXqkYZIOUkdFx6ueBSdw5b8Ao4gsFuJc-rt8d_tymWwXmyQ8iO-h5HirtseaNEw8th4f8oSK1Fq4QpqDyiLsWcE3m7TWHAtC-QPSizG_ugzB6UWWhsUVZSr04DdquBuj-Z344K8OYEYHbY-4SjC_kv10gFWh42fX3kPEaL61SYu69lki7eleBKFeLiSFC57X2gZLMLNDrqQiI32S6Gf676C90twCY</recordid><startdate>20120901</startdate><enddate>20120901</enddate><creator>Kim, Woo-Chan</creator><creator>Lee, Kang-Hoon</creator><creator>Shin, Kyung-Seop</creator><creator>You, Ri-Na</creator><creator>Lee, Young-Kwan</creator><creator>Cho, Kiho</creator><creator>Cho, Dong-Ho</creator><general>Elsevier Inc</general><general>Elsevier</general><scope>6I.</scope><scope>AAFTH</scope><scope>FBQ</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope></search><sort><creationdate>20120901</creationdate><title>REMiner-II: A tool for rapid identification and configuration of repetitive element arrays from large mammalian chromosomes as a single query</title><author>Kim, Woo-Chan ; Lee, Kang-Hoon ; Shin, Kyung-Seop ; You, Ri-Na ; Lee, Young-Kwan ; Cho, Kiho ; Cho, Dong-Ho</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c491t-2e823f7e565cea88d0d2b3ae082fc946480e4c30d13f37135dca90f401a08adb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Algorithms</topic><topic>Animals</topic><topic>Biological and medical sciences</topic><topic>Chromosome-wide</topic><topic>chromosomes</topic><topic>Chromosomes - genetics</topic><topic>Computational Biology - methods</topic><topic>Data Mining - methods</topic><topic>Databases, Genetic</topic><topic>Diverse techniques</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>genes</topic><topic>Genes. Genome</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>Genome, Human</topic><topic>Humans</topic><topic>Internet</topic><topic>Mammalian genome</topic><topic>Mammals - genetics</topic><topic>Mice</topic><topic>Mining</topic><topic>Molecular and cellular biology</topic><topic>Molecular genetics</topic><topic>Oligonucleotide Array Sequence Analysis - methods</topic><topic>RE array</topic><topic>REMiner-II</topic><topic>Repetitive element</topic><topic>Repetitive Sequences, Nucleic Acid</topic><topic>Sequence Alignment - methods</topic><topic>Software</topic><topic>Species Specificity</topic><topic>Time Factors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kim, Woo-Chan</creatorcontrib><creatorcontrib>Lee, Kang-Hoon</creatorcontrib><creatorcontrib>Shin, Kyung-Seop</creatorcontrib><creatorcontrib>You, Ri-Na</creatorcontrib><creatorcontrib>Lee, Young-Kwan</creatorcontrib><creatorcontrib>Cho, Kiho</creatorcontrib><creatorcontrib>Cho, Dong-Ho</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><jtitle>Genomics (San Diego, Calif.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kim, Woo-Chan</au><au>Lee, Kang-Hoon</au><au>Shin, Kyung-Seop</au><au>You, Ri-Na</au><au>Lee, Young-Kwan</au><au>Cho, Kiho</au><au>Cho, Dong-Ho</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>REMiner-II: A tool for rapid identification and configuration of repetitive element arrays from large mammalian chromosomes as a single query</atitle><jtitle>Genomics (San Diego, Calif.)</jtitle><addtitle>Genomics</addtitle><date>2012-09-01</date><risdate>2012</risdate><volume>100</volume><issue>3</issue><spage>131</spage><epage>140</epage><pages>131-140</pages><issn>0888-7543</issn><eissn>1089-8646</eissn><abstract>Genes occupy ~3% of the human and mouse genomes whereas repetitive elements (REs), whose biologic functions are largely uncharacterized, constitute greater than 50%. A heterogeneous population of RE arrays (arrangement structures) is formed by combinations of various REs in mammalian genomes. In this study, REMiner-II was refined from the original REMiner for a more efficient identification and configuration of RE arrays from large queries (e.g., human chromosomes) using an unbiased self-alignment protocol. Chromosome-wide RE array profiles for the entire sets of human and mouse chromosomes were obtained using REMiner-II on a personal computer. REMiner-II provides 10 adjustable parameters and three data output modes to accommodate different experimental settings and/or goals. Examination of the human and mouse chromosome data using the REMiner-II viewer revealed species-specific libraries of complexly organized RE arrays. In conclusion, REMiner-II is an efficient tool for chromosome-wide identification and characterization of RE arrays from mammalian genomes.</abstract><cop>Amsterdam</cop><pub>Elsevier Inc</pub><pmid>22750555</pmid><doi>10.1016/j.ygeno.2012.06.006</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Access via ScienceDirect (Elsevier); EZB-FREE-00999 freely available EZB journals |
| subjects | Algorithms Animals Biological and medical sciences Chromosome-wide chromosomes Chromosomes - genetics Computational Biology - methods Data Mining - methods Databases, Genetic Diverse techniques Fundamental and applied biological sciences. Psychology genes Genes. Genome Genetics of eukaryotes. Biological and molecular evolution Genome, Human Humans Internet Mammalian genome Mammals - genetics Mice Mining Molecular and cellular biology Molecular genetics Oligonucleotide Array Sequence Analysis - methods RE array REMiner-II Repetitive element Repetitive Sequences, Nucleic Acid Sequence Alignment - methods Software Species Specificity Time Factors |
| title | REMiner-II: A tool for rapid identification and configuration of repetitive element arrays from large mammalian chromosomes as a single query |
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