ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants
Identifieur interne : 000885 ( Pmc/Checkpoint ); précédent : 000884; suivant : 000886ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants
Auteurs : Aditi Kapil [Inde] ; Piyush Kant Rai [Inde] ; Asheesh Shanker [Inde]Source :
- Database: The Journal of Biological Databases and Curation [ 1758-0463 ] ; 2014.
Abstract
Simple sequence repeats (SSRs) are regions in DNA sequence that contain repeating motifs of length 1–6 nucleotides. These repeats are ubiquitously present and are found in both coding and non-coding regions of genome. A total of 534 complete chloroplast genome sequences (as on 18 September 2014) of Viridiplantae are available at NCBI organelle genome resource. It provides opportunity to mine these genomes for the detection of SSRs and store them in the form of a database. In an attempt to properly manage and retrieve chloroplastic SSRs, we designed ChloroSSRdb which is a relational database developed using SQL server 2008 and accessed through ASP.NET. It provides information of all the three types (perfect, imperfect and compound) of SSRs. At present, ChloroSSRdb contains 124 430 mined SSRs, with majority lying in non-coding region. Out of these, PCR primers were designed for 118 249 SSRs. Tetranucleotide repeats (47 079) were found to be the most frequent repeat type, whereas hexanucleotide repeats (6414) being the least abundant. Additionally, in each species statistical analyses were performed to calculate relative frequency, correlation coefficient and chi-square statistics of perfect and imperfect SSRs. In accordance with the growing interest in SSR studies, ChloroSSRdb will prove to be a useful resource in developing genetic markers, phylogenetic analysis, genetic mapping, etc. Moreover, it will serve as a ready reference for mined SSRs in available chloroplast genomes of green plants.
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DOI: 10.1093/database/bau107
PubMed: 25380781
PubMed Central: 4224265
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These repeats are ubiquitously present and are found in both coding and non-coding regions of genome. A total of 534 complete chloroplast genome sequences (as on 18 September 2014) of Viridiplantae are available at NCBI organelle genome resource. It provides opportunity to mine these genomes for the detection of SSRs and store them in the form of a database. In an attempt to properly manage and retrieve chloroplastic SSRs, we designed ChloroSSRdb which is a relational database developed using SQL server 2008 and accessed through ASP.NET. It provides information of all the three types (perfect, imperfect and compound) of SSRs. At present, ChloroSSRdb contains 124 430 mined SSRs, with majority lying in non-coding region. Out of these, PCR primers were designed for 118 249 SSRs. Tetranucleotide repeats (47 079) were found to be the most frequent repeat type, whereas hexanucleotide repeats (6414) being the least abundant. Additionally, in each species statistical analyses were performed to calculate relative frequency, correlation coefficient and chi-square statistics of perfect and imperfect SSRs. In accordance with the growing interest in SSR studies, ChloroSSRdb will prove to be a useful resource in developing genetic markers, phylogenetic analysis, genetic mapping, etc. Moreover, it will serve as a ready reference for mined SSRs in available chloroplast genomes of green plants.</p><p><bold>Database URL:</bold><ext-link ext-link-type="uri" xlink:href="http://www.compubio.in/chlorossrdb/">www.compubio.in/chlorossrdb/</ext-link></p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Kabeya, Y" uniqKey="Kabeya Y">Y. Kabeya</name></author><author><name sortKey="Miyagishima, S Y" uniqKey="Miyagishima S">S.Y. Miyagishima</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wicke, S" uniqKey="Wicke S">S. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Database (Oxford)</journal-id><journal-id journal-id-type="iso-abbrev">Database (Oxford)</journal-id><journal-id journal-id-type="publisher-id">databa</journal-id><journal-id journal-id-type="hwp">databa</journal-id><journal-title-group><journal-title>Database: The Journal of Biological Databases and Curation</journal-title></journal-title-group><issn pub-type="epub">1758-0463</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25380781</article-id><article-id pub-id-type="pmc">4224265</article-id><article-id pub-id-type="doi">10.1093/database/bau107</article-id><article-id pub-id-type="publisher-id">bau107</article-id><article-categories><subj-group subj-group-type="heading"><subject>Original Article</subject></subj-group></article-categories><title-group><article-title>ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Kapil</surname><given-names>Aditi</given-names></name><xref ref-type="aff" rid="bau107-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Rai</surname><given-names>Piyush Kant</given-names></name><xref ref-type="aff" rid="bau107-AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Shanker</surname><given-names>Asheesh</given-names></name><xref ref-type="aff" rid="bau107-AFF1"><sup>1</sup></xref><xref ref-type="corresp" rid="bau107-COR1">*</xref></contrib><aff id="bau107-AFF1"><sup>1</sup>Department of Bioinformatics, Banasthali University, Banasthali, Rajasthan 304022, India and<sup>2</sup>Department of Mathematics and Statistics, Banasthali University, Banasthali, Rajasthan 304022, India</aff></contrib-group><author-notes><corresp id="bau107-COR1">*Corresponding author: Tel: <phone>+91 9414478655</phone>; Fax: <fax>+91 1438 228649</fax>; Email: <email>ashomics@gmail.com</email></corresp><fn id="FN1"><p>Citation details: Kapil,A., Rai,P.K. and Shanker,A. ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants. <italic>Database</italic> (2014) Vol. 2014: article ID bau107; doi:10.1093/database/bau107</p></fn></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>06</day><month>11</month><year>2014</year></pub-date><pub-date pub-type="pmc-release"><day>06</day><month>11</month><year>2014</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>2014</volume><elocation-id>bau107</elocation-id><history><date date-type="received"><day>25</day><month>7</month><year>2014</year></date><date date-type="rev-recd"><day>19</day><month>9</month><year>2014</year></date><date date-type="accepted"><day>8</day><month>10</month><year>2014</year></date></history><permissions><copyright-statement>© The Author(s) 2014. Published by Oxford University Press.</copyright-statement><copyright-year>2014</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>Simple sequence repeats (SSRs) are regions in DNA sequence that contain repeating motifs of length 1–6 nucleotides. These repeats are ubiquitously present and are found in both coding and non-coding regions of genome. A total of 534 complete chloroplast genome sequences (as on 18 September 2014) of Viridiplantae are available at NCBI organelle genome resource. It provides opportunity to mine these genomes for the detection of SSRs and store them in the form of a database. In an attempt to properly manage and retrieve chloroplastic SSRs, we designed ChloroSSRdb which is a relational database developed using SQL server 2008 and accessed through ASP.NET. It provides information of all the three types (perfect, imperfect and compound) of SSRs. At present, ChloroSSRdb contains 124 430 mined SSRs, with majority lying in non-coding region. Out of these, PCR primers were designed for 118 249 SSRs. Tetranucleotide repeats (47 079) were found to be the most frequent repeat type, whereas hexanucleotide repeats (6414) being the least abundant. Additionally, in each species statistical analyses were performed to calculate relative frequency, correlation coefficient and chi-square statistics of perfect and imperfect SSRs. In accordance with the growing interest in SSR studies, ChloroSSRdb will prove to be a useful resource in developing genetic markers, phylogenetic analysis, genetic mapping, etc. Moreover, it will serve as a ready reference for mined SSRs in available chloroplast genomes of green plants.</p><p><bold>Database URL:</bold><ext-link ext-link-type="uri" xlink:href="http://www.compubio.in/chlorossrdb/">www.compubio.in/chlorossrdb/</ext-link></p></abstract><counts><page-count count="5"></page-count></counts></article-meta></front></pmc><affiliations><list><country><li>Inde</li></country></list><tree><country name="Inde"><noRegion><name sortKey="Kapil, Aditi" sort="Kapil, Aditi" uniqKey="Kapil A" first="Aditi" last="Kapil">Aditi Kapil</name></noRegion><name sortKey="Rai, Piyush Kant" sort="Rai, Piyush Kant" uniqKey="Rai P" first="Piyush Kant" last="Rai">Piyush Kant Rai</name><name sortKey="Shanker, Asheesh" sort="Shanker, Asheesh" uniqKey="Shanker A" first="Asheesh" last="Shanker">Asheesh Shanker</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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