Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding
Identifieur interne : 000E84 ( Main/Merge ); précédent : 000E83; suivant : 000E85Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding
Auteurs : Wayne K. Dawson ; Kazuya Fujiwara ; Gota KawaiSource :
- PLoS ONE [ 1932-6203 ] ; 2007.
Abstract
Predicting RNA secondary structure is often the first step to determining the structure of RNA. Prediction approaches have historically avoided searching for pseudoknots because of the extreme combinatorial and time complexity of the problem. Yet neglecting pseudoknots limits the utility of such approaches. Here, an algorithm utilizing structure mapping and thermodynamics is introduced for RNA pseudoknot prediction that finds the minimum free energy and identifies information about the flexibility of the RNA. The heuristic approach takes advantage of the 5′ to 3′ folding direction of many biological RNA molecules and is consistent with the hierarchical folding hypothesis and the contact order model. Mapping methods are used to build and analyze the folded structure for pseudoknots and to add important 3D structural considerations. The program can predict some well known pseudoknot structures correctly. The results of this study suggest that many functional RNA sequences are optimized for proper folding. They also suggest directions we can proceed in the future to achieve even better results.
Url:
DOI: 10.1371/journal.pone.0000905
PubMed: 17878940
PubMed Central: 1975678
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000691
- to stream Pmc, to step Curation: 000691
- to stream Pmc, to step Checkpoint: 000667
- to stream Ncbi, to step Merge: 000103
- to stream Ncbi, to step Curation: 000103
- to stream Ncbi, to step Checkpoint: 000103
Links to Exploration step
PMC:1975678Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding</title>
<author><name sortKey="Dawson, Wayne K" sort="Dawson, Wayne K" uniqKey="Dawson W" first="Wayne K." last="Dawson">Wayne K. Dawson</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Fujiwara, Kazuya" sort="Fujiwara, Kazuya" uniqKey="Fujiwara K" first="Kazuya" last="Fujiwara">Kazuya Fujiwara</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Kawai, Gota" sort="Kawai, Gota" uniqKey="Kawai G" first="Gota" last="Kawai">Gota Kawai</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">17878940</idno>
<idno type="pmc">1975678</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1975678</idno>
<idno type="RBID">PMC:1975678</idno>
<idno type="doi">10.1371/journal.pone.0000905</idno>
<date when="2007">2007</date>
<idno type="wicri:Area/Pmc/Corpus">000691</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000691</idno>
<idno type="wicri:Area/Pmc/Curation">000691</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000691</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000667</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000667</idno>
<idno type="wicri:Area/Ncbi/Merge">000103</idno>
<idno type="wicri:Area/Ncbi/Curation">000103</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">000103</idno>
<idno type="wicri:Area/Main/Merge">000E84</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding</title>
<author><name sortKey="Dawson, Wayne K" sort="Dawson, Wayne K" uniqKey="Dawson W" first="Wayne K." last="Dawson">Wayne K. Dawson</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Fujiwara, Kazuya" sort="Fujiwara, Kazuya" uniqKey="Fujiwara K" first="Kazuya" last="Fujiwara">Kazuya Fujiwara</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
<author><name sortKey="Kawai, Gota" sort="Kawai, Gota" uniqKey="Kawai G" first="Gota" last="Kawai">Gota Kawai</name>
<affiliation><nlm:aff id="aff1"></nlm:aff>
</affiliation>
</author>
</analytic>
<series><title level="j">PLoS ONE</title>
<idno type="eISSN">1932-6203</idno>
<imprint><date when="2007">2007</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>Predicting RNA secondary structure is often the first step to determining the structure of RNA. Prediction approaches have historically avoided searching for pseudoknots because of the extreme combinatorial and time complexity of the problem. Yet neglecting pseudoknots limits the utility of such approaches. Here, an algorithm utilizing structure mapping and thermodynamics is introduced for RNA pseudoknot prediction that finds the minimum free energy and identifies information about the flexibility of the RNA. The heuristic approach takes advantage of the 5′ to 3′ folding direction of many biological RNA molecules and is consistent with the hierarchical folding hypothesis and the contact order model. Mapping methods are used to build and analyze the folded structure for pseudoknots and to add important 3D structural considerations. The program can predict some well known pseudoknot structures correctly. The results of this study suggest that many functional RNA sequences are optimized for proper folding. They also suggest directions we can proceed in the future to achieve even better results.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Reeder, J" uniqKey="Reeder J">J Reeder</name>
</author>
<author><name sortKey="Hochsmann, M" uniqKey="Hochsmann M">M Hochsmann</name>
</author>
<author><name sortKey="Rehmsmeier, M" uniqKey="Rehmsmeier M">M Rehmsmeier</name>
</author>
<author><name sortKey="Voss, B" uniqKey="Voss B">B Voss</name>
</author>
<author><name sortKey="Giegerich, R" uniqKey="Giegerich R">R Giegerich</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hendrix, Dk" uniqKey="Hendrix D">DK Hendrix</name>
</author>
<author><name sortKey="Brenner, Se" uniqKey="Brenner S">SE Brenner</name>
</author>
<author><name sortKey="Holbrook, Sr" uniqKey="Holbrook S">SR Holbrook</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Xayaphoummine, A" uniqKey="Xayaphoummine A">A Xayaphoummine</name>
</author>
<author><name sortKey="Bucher, T" uniqKey="Bucher T">T Bucher</name>
</author>
<author><name sortKey="Thalmann, F" uniqKey="Thalmann F">F Thalmann</name>
</author>
<author><name sortKey="Isambert, H" uniqKey="Isambert H">H Isambert</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lyngso, Rb" uniqKey="Lyngso R">RB Lyngso</name>
</author>
<author><name sortKey="Pedersen, Ns" uniqKey="Pedersen N">NS Pedersen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kolk, Mh" uniqKey="Kolk M">MH Kolk</name>
</author>
<author><name sortKey="Van Der Graaf, M" uniqKey="Van Der Graaf M">M van der Graaf</name>
</author>
<author><name sortKey="Wijmenga, Ss" uniqKey="Wijmenga S">SS Wijmenga</name>
</author>
<author><name sortKey="Pleij, Cw" uniqKey="Pleij C">CW Pleij</name>
</author>
<author><name sortKey="Heus, Ha" uniqKey="Heus H">HA Heus</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Baird, Sd" uniqKey="Baird S">SD Baird</name>
</author>
<author><name sortKey="Turcotte, M" uniqKey="Turcotte M">M Turcotte</name>
</author>
<author><name sortKey="Korneluk, Rg" uniqKey="Korneluk R">RG Korneluk</name>
</author>
<author><name sortKey="Holcik, M" uniqKey="Holcik M">M Holcik</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Felden, B" uniqKey="Felden B">B Felden</name>
</author>
<author><name sortKey="Florentz, C" uniqKey="Florentz C">C Florentz</name>
</author>
<author><name sortKey="Giege, R" uniqKey="Giege R">R Giege</name>
</author>
<author><name sortKey="Westhof, E" uniqKey="Westhof E">E Westhof</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Su, M C" uniqKey="Su M">M-C Su</name>
</author>
<author><name sortKey="Chang, C T" uniqKey="Chang C">C-T Chang</name>
</author>
<author><name sortKey="Chu, C H" uniqKey="Chu C">C-H Chu</name>
</author>
<author><name sortKey="Tsai, C H" uniqKey="Tsai C">C-H Tsai</name>
</author>
<author><name sortKey="Chang, Ky" uniqKey="Chang K">KY Chang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Plant, Ep" uniqKey="Plant E">EP Plant</name>
</author>
<author><name sortKey="Perez Alvarado, Gc" uniqKey="Perez Alvarado G">GC Perez-Alvarado</name>
</author>
<author><name sortKey="Jacobs, Jl" uniqKey="Jacobs J">JL Jacobs</name>
</author>
<author><name sortKey="Mukhopadhyay, B" uniqKey="Mukhopadhyay B">B Mukhopadhyay</name>
</author>
<author><name sortKey="Henning, M" uniqKey="Henning M">M Henning</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Tumpey, Tm" uniqKey="Tumpey T">TM Tumpey</name>
</author>
<author><name sortKey="Maines, Tr" uniqKey="Maines T">TR Maines</name>
</author>
<author><name sortKey="Van Hoeven, N" uniqKey="Van Hoeven N">N Van Hoeven</name>
</author>
<author><name sortKey="Glaser, L" uniqKey="Glaser L">L Glaser</name>
</author>
<author><name sortKey="Sol Rzano, A" uniqKey="Sol Rzano A">A Solórzano</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Huttenhofer, A" uniqKey="Huttenhofer A">A Huttenhofer</name>
</author>
<author><name sortKey="Schattner, P" uniqKey="Schattner P">P Schattner</name>
</author>
<author><name sortKey="Polacek, N" uniqKey="Polacek N">N Polacek</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Schultes, Ea" uniqKey="Schultes E">EA Schultes</name>
</author>
<author><name sortKey="Spasic, A" uniqKey="Spasic A">A Spasic</name>
</author>
<author><name sortKey="Mohanty, U" uniqKey="Mohanty U">U Mohanty</name>
</author>
<author><name sortKey="Bartel, Dp" uniqKey="Bartel D">DP Bartel</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Dawson, W" uniqKey="Dawson W">W Dawson</name>
</author>
<author><name sortKey="Fujiwara, K" uniqKey="Fujiwara K">K Fujiwara</name>
</author>
<author><name sortKey="Futamura, Y" uniqKey="Futamura Y">Y Futamura</name>
</author>
<author><name sortKey="Yamamoto, K" uniqKey="Yamamoto K">K Yamamoto</name>
</author>
<author><name sortKey="Kawai, G" uniqKey="Kawai G">G Kawai</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Eddy, Sr" uniqKey="Eddy S">SR Eddy</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bruccoleri, R" uniqKey="Bruccoleri R">R Bruccoleri</name>
</author>
<author><name sortKey="Heinrich, G" uniqKey="Heinrich G">G Heinrich</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kumar, Pk" uniqKey="Kumar P">PK Kumar</name>
</author>
<author><name sortKey="Suh, Ya" uniqKey="Suh Y">YA Suh</name>
</author>
<author><name sortKey="Miyashiro, H" uniqKey="Miyashiro H">H Miyashiro</name>
</author>
<author><name sortKey="Nishikawa, F" uniqKey="Nishikawa F">F Nishikawa</name>
</author>
<author><name sortKey="Kawakami, J" uniqKey="Kawakami J">J Kawakami</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Nameki, N" uniqKey="Nameki N">N Nameki</name>
</author>
<author><name sortKey="Chattopadhyay, P" uniqKey="Chattopadhyay P">P Chattopadhyay</name>
</author>
<author><name sortKey="Himeno, H" uniqKey="Himeno H">H Himeno</name>
</author>
<author><name sortKey="Muto, A" uniqKey="Muto A">A Muto</name>
</author>
<author><name sortKey="Kawai, G" uniqKey="Kawai G">G Kawai</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mandal, M" uniqKey="Mandal M">M Mandal</name>
</author>
<author><name sortKey="Boese, B" uniqKey="Boese B">B Boese</name>
</author>
<author><name sortKey="Barrick, Je" uniqKey="Barrick J">JE Barrick</name>
</author>
<author><name sortKey="Winkler, Wc" uniqKey="Winkler W">WC Winkler</name>
</author>
<author><name sortKey="Breaker, Rr" uniqKey="Breaker R">RR Breaker</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Cate, Jh" uniqKey="Cate J">JH Cate</name>
</author>
<author><name sortKey="Hanna, Rl" uniqKey="Hanna R">RL Hanna</name>
</author>
<author><name sortKey="Doudna, Ja" uniqKey="Doudna J">JA Doudna</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Flory, Pj" uniqKey="Flory P">PJ Flory</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Schlax, Pj" uniqKey="Schlax P">PJ Schlax</name>
</author>
<author><name sortKey="Xavier, Ka" uniqKey="Xavier K">KA Xavier</name>
</author>
<author><name sortKey="Gluick, Tc" uniqKey="Gluick T">TC Gluick</name>
</author>
<author><name sortKey="Draper, De" uniqKey="Draper D">DE Draper</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Misra, Vk" uniqKey="Misra V">VK Misra</name>
</author>
<author><name sortKey="Draper, De" uniqKey="Draper D">DE Draper</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Torres Larios, A" uniqKey="Torres Larios A">A Torres-Larios</name>
</author>
<author><name sortKey="Swinger, Kk" uniqKey="Swinger K">KK Swinger</name>
</author>
<author><name sortKey="Krasilnikov, As" uniqKey="Krasilnikov A">AS Krasilnikov</name>
</author>
<author><name sortKey="Pan, T" uniqKey="Pan T">T Pan</name>
</author>
<author><name sortKey="Mondragon, A" uniqKey="Mondragon A">A Mondragon</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lescoute, A" uniqKey="Lescoute A">A Lescoute</name>
</author>
<author><name sortKey="Westhof, E" uniqKey="Westhof E">E Westhof</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Tinoco, I" uniqKey="Tinoco I">I Tinoco</name>
</author>
<author><name sortKey="Bustamante, C" uniqKey="Bustamante C">C Bustamante</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Doshi, Kj" uniqKey="Doshi K">KJ Doshi</name>
</author>
<author><name sortKey="Cannone, Jj" uniqKey="Cannone J">JJ Cannone</name>
</author>
<author><name sortKey="Cobaugh, Cw" uniqKey="Cobaugh C">CW Cobaugh</name>
</author>
<author><name sortKey="Gutell, Rr" uniqKey="Gutell R">RR Gutell</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Makarov, De" uniqKey="Makarov D">DE Makarov</name>
</author>
<author><name sortKey="Keller, Ca" uniqKey="Keller C">CA Keller</name>
</author>
<author><name sortKey="Plaxco, Kw" uniqKey="Plaxco K">KW Plaxco</name>
</author>
<author><name sortKey="Metiu, H" uniqKey="Metiu H">H Metiu</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sosnick, Tr" uniqKey="Sosnick T">TR Sosnick</name>
</author>
<author><name sortKey="Pan T, J" uniqKey="Pan T J">J Pan T</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Cao, S" uniqKey="Cao S">S Cao</name>
</author>
<author><name sortKey="Chen, S J" uniqKey="Chen S">S-J Chen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rivas, E" uniqKey="Rivas E">E Rivas</name>
</author>
<author><name sortKey="Eddy, Sr" uniqKey="Eddy S">SR Eddy</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Sante/explor/CovidV1/Data/Main/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000E84 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Merge/biblio.hfd -nk 000E84 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Wicri/Sante |area= CovidV1 |flux= Main |étape= Merge |type= RBID |clé= PMC:1975678 |texte= Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Merge/RBID.i -Sk "pubmed:17878940" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Merge/biblio.hfd \ | NlmPubMed2Wicri -a CovidV1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |