ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants
Identifieur interne : 001896 ( Ncbi/Checkpoint ); précédent : 001895; suivant : 001897ChloroSSRdb: 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.
Url:
DOI: 10.1093/database/bau107
PubMed: 25380781
PubMed Central: 4224265
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000E77
- to stream Pmc, to step Curation: 000E76
- to stream Pmc, to step Checkpoint: 000885
- to stream Ncbi, to step Merge: 001896
- to stream Ncbi, to step Curation: 001896
Links to Exploration step
PMC:4224265Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants</title><author><name sortKey="Kapil, Aditi" sort="Kapil, Aditi" uniqKey="Kapil A" first="Aditi" last="Kapil">Aditi Kapil</name><affiliation wicri:level="1"><nlm:aff wicri:cut=" and" id="bau107-AFF1">Department of Bioinformatics, Banasthali University, Banasthali, Rajasthan 304022, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Bioinformatics, Banasthali University, Banasthali, Rajasthan 304022</wicri:regionArea><wicri:noRegion>Rajasthan 304022</wicri:noRegion></affiliation></author><author><name sortKey="Rai, Piyush Kant" sort="Rai, Piyush Kant" uniqKey="Rai P" first="Piyush Kant" last="Rai">Piyush Kant Rai</name><affiliation wicri:level="1"><nlm:aff id="bau107-AFF1">Department of Mathematics and Statistics, Banasthali University, Banasthali, Rajasthan 304022, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Mathematics and Statistics, Banasthali University, Banasthali, Rajasthan 304022</wicri:regionArea><wicri:noRegion>Rajasthan 304022</wicri:noRegion></affiliation></author><author><name sortKey="Shanker, Asheesh" sort="Shanker, Asheesh" uniqKey="Shanker A" first="Asheesh" last="Shanker">Asheesh Shanker</name><affiliation wicri:level="1"><nlm:aff wicri:cut=" and" id="bau107-AFF1">Department of Bioinformatics, Banasthali University, Banasthali, Rajasthan 304022, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Bioinformatics, Banasthali University, Banasthali, Rajasthan 304022</wicri:regionArea><wicri:noRegion>Rajasthan 304022</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25380781</idno><idno type="pmc">4224265</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224265</idno><idno type="RBID">PMC:4224265</idno><idno type="doi">10.1093/database/bau107</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000E77</idno><idno type="wicri:Area/Pmc/Curation">000E76</idno><idno type="wicri:Area/Pmc/Checkpoint">000885</idno><idno type="wicri:Area/Ncbi/Merge">001896</idno><idno type="wicri:Area/Ncbi/Curation">001896</idno><idno type="wicri:Area/Ncbi/Checkpoint">001896</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants</title><author><name sortKey="Kapil, Aditi" sort="Kapil, Aditi" uniqKey="Kapil A" first="Aditi" last="Kapil">Aditi Kapil</name><affiliation wicri:level="1"><nlm:aff wicri:cut=" and" id="bau107-AFF1">Department of Bioinformatics, Banasthali University, Banasthali, Rajasthan 304022, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Bioinformatics, Banasthali University, Banasthali, Rajasthan 304022</wicri:regionArea><wicri:noRegion>Rajasthan 304022</wicri:noRegion></affiliation></author><author><name sortKey="Rai, Piyush Kant" sort="Rai, Piyush Kant" uniqKey="Rai P" first="Piyush Kant" last="Rai">Piyush Kant Rai</name><affiliation wicri:level="1"><nlm:aff id="bau107-AFF1">Department of Mathematics and Statistics, Banasthali University, Banasthali, Rajasthan 304022, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Mathematics and Statistics, Banasthali University, Banasthali, Rajasthan 304022</wicri:regionArea><wicri:noRegion>Rajasthan 304022</wicri:noRegion></affiliation></author><author><name sortKey="Shanker, Asheesh" sort="Shanker, Asheesh" uniqKey="Shanker A" first="Asheesh" last="Shanker">Asheesh Shanker</name><affiliation wicri:level="1"><nlm:aff wicri:cut=" and" id="bau107-AFF1">Department of Bioinformatics, Banasthali University, Banasthali, Rajasthan 304022, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Bioinformatics, Banasthali University, Banasthali, Rajasthan 304022</wicri:regionArea><wicri:noRegion>Rajasthan 304022</wicri:noRegion></affiliation></author></analytic><series><title level="j">Database: The Journal of Biological Databases and Curation</title><idno type="eISSN">1758-0463</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><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></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. Wicke</name></author><author><name sortKey="Schneeweiss, G M" uniqKey="Schneeweiss G">G.M. Schneeweiss</name></author><author><name sortKey="Depamphilis, C W" uniqKey="Depamphilis C">C.W. dePamphilis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Neuhaus, H E" uniqKey="Neuhaus H">H.E. Neuhaus</name></author><author><name sortKey="Emes, M J" uniqKey="Emes M">M.J. Emes</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Olmstead, R G" uniqKey="Olmstead R">R.G. Olmstead</name></author><author><name sortKey="Palmer, J D" uniqKey="Palmer J">J.D. Palmer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shanker, A" uniqKey="Shanker A">A. Shanker</name></author><author><name sortKey="Sharma, V" uniqKey="Sharma V">V. Sharma</name></author><author><name sortKey="Daniell, H" uniqKey="Daniell H">H. Daniell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shanker, A" uniqKey="Shanker A">A. Shanker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shanker, A" uniqKey="Shanker A">A. Shanker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shanker, A" uniqKey="Shanker A">A. Shanker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shanker, A" uniqKey="Shanker A">A. Shanker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Toth, G" uniqKey="Toth G">G. Toth</name></author><author><name sortKey="Gaspari, Z" uniqKey="Gaspari Z">Z. Gaspari</name></author><author><name sortKey="Zurka, J" uniqKey="Zurka J">J. Zurka</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tautz, D" uniqKey="Tautz D">D. Tautz</name></author><author><name sortKey="Schlotterer, C" uniqKey="Schlotterer C">C. Schlotterer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hancock, J M" uniqKey="Hancock J">J.M. Hancock</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Squirrell, J" uniqKey="Squirrell J">J. Squirrell</name></author><author><name sortKey="Hollingsworth, P M" uniqKey="Hollingsworth P">P.M. Hollingsworth</name></author><author><name sortKey="Woodhead, M" uniqKey="Woodhead M">M. Woodhead</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Botstein, D" uniqKey="Botstein D">D. Botstein</name></author><author><name sortKey="White, R L" uniqKey="White R">R.L. White</name></author><author><name sortKey="Skolnick, M" uniqKey="Skolnick M">M. Skolnick</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sung, W" uniqKey="Sung W">W. Sung</name></author><author><name sortKey="Tucker, A" uniqKey="Tucker A">A. Tucker</name></author><author><name sortKey="Bergeron, R D" uniqKey="Bergeron R">R.D. Bergeron</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kashi, Y" uniqKey="Kashi Y">Y. Kashi</name></author><author><name sortKey="King, D G" uniqKey="King D">D.G. King</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Farazi, T A" uniqKey="Farazi T">T.A. Farazi</name></author><author><name sortKey="Juranek, S A" uniqKey="Juranek S">S.A. Juranek</name></author><author><name sortKey="Tuschl, T" uniqKey="Tuschl T">T. Tuschl</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Provan, J" uniqKey="Provan J">J. Provan</name></author><author><name sortKey="Powell, W" uniqKey="Powell W">W. Powell</name></author><author><name sortKey="Hollingsworth, P M" uniqKey="Hollingsworth P">P.M. Hollingsworth</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shanker, A" uniqKey="Shanker A">A. Shanker</name></author><author><name sortKey="Bhargava, A" uniqKey="Bhargava A">A. Bhargava</name></author><author><name sortKey="Bajpai, R" uniqKey="Bajpai R">R. Bajpai</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shanker, A" uniqKey="Shanker A">A. Shanker</name></author><author><name sortKey="Singh, A" uniqKey="Singh A">A. Singh</name></author><author><name sortKey="Sharma, V" uniqKey="Sharma V">V. Sharma</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sreenu, V B" uniqKey="Sreenu V">V.B. Sreenu</name></author><author><name sortKey="Alevoor, V" uniqKey="Alevoor V">V. Alevoor</name></author><author><name sortKey="Nagaraju, J" uniqKey="Nagaraju J">J. Nagaraju</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Blenda, A" uniqKey="Blenda A">A. Blenda</name></author><author><name sortKey="Scheffler, J" uniqKey="Scheffler J">J. Scheffler</name></author><author><name sortKey="Scheffler, B" uniqKey="Scheffler B">B. Scheffler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Aishwarya, V" uniqKey="Aishwarya V">V. Aishwarya</name></author><author><name sortKey="Grover, A" uniqKey="Grover A">A. Grover</name></author><author><name sortKey="Sharma, P C" uniqKey="Sharma P">P.C. Sharma</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sarika" uniqKey="Sarika">Sarika</name></author><author><name sortKey="Arora, V" uniqKey="Arora V">V. Arora</name></author><author><name sortKey="Iquebal, M A" uniqKey="Iquebal M">M.A. Iquebal</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sablok, G" uniqKey="Sablok G">G. Sablok</name></author><author><name sortKey="Mudunuri, S B" uniqKey="Mudunuri S">S.B. Mudunuri</name></author><author><name sortKey="Patnana, S" uniqKey="Patnana S">S. Patnana</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kumar, M" uniqKey="Kumar M">M. Kumar</name></author><author><name sortKey="Kapil, A" uniqKey="Kapil A">A. Kapil</name></author><author><name sortKey="Shanker, A" uniqKey="Shanker A">A. Shanker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mudunuri, S B" uniqKey="Mudunuri S">S.B. Mudunuri</name></author><author><name sortKey="Nagarajaram, H A" uniqKey="Nagarajaram H">H.A. Nagarajaram</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Untergrasser, A" uniqKey="Untergrasser A">A. Untergrasser</name></author><author><name sortKey="Cutcutache, I" uniqKey="Cutcutache I">I. Cutcutache</name></author><author><name sortKey="Koressaar, T" uniqKey="Koressaar T">T. Koressaar</name></author></analytic></biblStruct></listBibl></div1></back></TEI><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)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Bois/explor/OrangerV1/Data/Ncbi/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001896 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Checkpoint/biblio.hfd -nk 001896 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Bois
|area= OrangerV1
|flux= Ncbi
|étape= Checkpoint
|type= RBID
|clé= PMC:4224265
|texte= ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Checkpoint/RBID.i -Sk "pubmed:25380781" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Checkpoint/biblio.hfd \
| NlmPubMed2Wicri -a OrangerV1
| This area was generated with Dilib version V0.6.25. |  |