SwiSpot: modeling riboswitches by spotting out switching sequences
Riboswitches are cis-regulatory elements in mRNA, mostly found in Bacteria, which exhibit two main secondary structure conformations. Although one of them prevents the gene from being expressed, the other conformation allows its expression, and this switching process is typically driven by the prese...
Saved in:
Published in | Bioinformatics (Oxford, England) Vol. 32; no. 21; pp. 3252 - 3259 |
---|---|
Main Authors | , , , |
Format | Journal Article |
Language | English |
Published |
England
01.11.2016
|
Subjects | |
Online Access | Get full text |
Cover
Loading…
Abstract | Riboswitches are cis-regulatory elements in mRNA, mostly found in Bacteria, which exhibit two main secondary structure conformations. Although one of them prevents the gene from being expressed, the other conformation allows its expression, and this switching process is typically driven by the presence of a specific ligand. Although there are a handful of known riboswitches, our knowledge in this field has been greatly limited due to our inability to identify their alternate structures from their sequences. Indeed, current methods are not able to predict the presence of the two functionally distinct conformations just from the knowledge of the plain RNA nucleotide sequence. Whether this would be possible, for which cases, and what prediction accuracy can be achieved, are currently open questions.
Here we show that the two alternate secondary structures of riboswitches can be accurately predicted once the 'switching sequence' of the riboswitch has been properly identified. The proposed SwiSpot approach is capable of identifying the switching sequence inside a putative, complete riboswitch sequence, on the basis of pairing behaviors, which are evaluated on proper sets of configurations. Moreover, it is able to model the switching behavior of riboswitches whose generated ensemble covers both alternate configurations. Beyond structural predictions, the approach can also be paired to homology-based riboswitch searches.
SwiSpot software, along with the reference dataset files, is available at: http://www.iet.unipi.it/a.bechini/swispot/Supplementary information: Supplementary data are available at Bioinformatics online.
a.bechini@ing.unipi.it. |
---|---|
AbstractList | Riboswitches are cis-regulatory elements in mRNA, mostly found in Bacteria, which exhibit two main secondary structure conformations. Although one of them prevents the gene from being expressed, the other conformation allows its expression, and this switching process is typically driven by the presence of a specific ligand. Although there are a handful of known riboswitches, our knowledge in this field has been greatly limited due to our inability to identify their alternate structures from their sequences. Indeed, current methods are not able to predict the presence of the two functionally distinct conformations just from the knowledge of the plain RNA nucleotide sequence. Whether this would be possible, for which cases, and what prediction accuracy can be achieved, are currently open questions.
Here we show that the two alternate secondary structures of riboswitches can be accurately predicted once the 'switching sequence' of the riboswitch has been properly identified. The proposed SwiSpot approach is capable of identifying the switching sequence inside a putative, complete riboswitch sequence, on the basis of pairing behaviors, which are evaluated on proper sets of configurations. Moreover, it is able to model the switching behavior of riboswitches whose generated ensemble covers both alternate configurations. Beyond structural predictions, the approach can also be paired to homology-based riboswitch searches.
SwiSpot software, along with the reference dataset files, is available at: http://www.iet.unipi.it/a.bechini/swispot/Supplementary information: Supplementary data are available at Bioinformatics online.
a.bechini@ing.unipi.it. MOTIVATIONRiboswitches are cis-regulatory elements in mRNA, mostly found in Bacteria, which exhibit two main secondary structure conformations. Although one of them prevents the gene from being expressed, the other conformation allows its expression, and this switching process is typically driven by the presence of a specific ligand. Although there are a handful of known riboswitches, our knowledge in this field has been greatly limited due to our inability to identify their alternate structures from their sequences. Indeed, current methods are not able to predict the presence of the two functionally distinct conformations just from the knowledge of the plain RNA nucleotide sequence. Whether this would be possible, for which cases, and what prediction accuracy can be achieved, are currently open questions.RESULTSHere we show that the two alternate secondary structures of riboswitches can be accurately predicted once the 'switching sequence' of the riboswitch has been properly identified. The proposed SwiSpot approach is capable of identifying the switching sequence inside a putative, complete riboswitch sequence, on the basis of pairing behaviors, which are evaluated on proper sets of configurations. Moreover, it is able to model the switching behavior of riboswitches whose generated ensemble covers both alternate configurations. Beyond structural predictions, the approach can also be paired to homology-based riboswitch searches.AVAILABILITY AND IMPLEMENTATIONSwiSpot software, along with the reference dataset files, is available at: http://www.iet.unipi.it/a.bechini/swispot/Supplementary information: Supplementary data are available at Bioinformatics online.CONTACTa.bechini@ing.unipi.it. Motivation: Riboswitches are cis-regulatory elements in mRNA, mostly found in Bacteria, which exhibit two main secondary structure conformations. Although one of them prevents the gene from being expressed, the other conformation allows its expression, and this switching process is typically driven by the presence of a specific ligand. Although there are a handful of known riboswitches, our knowledge in this field has been greatly limited due to our inability to identify their alternate structures from their sequences. Indeed, current methods are not able to predict the presence of the two functionally distinct conformations just from the knowledge of the plain RNA nucleotide sequence. Whether this would be possible, for which cases, and what prediction accuracy can be achieved, are currently open questions. Results: Here we show that the two alternate secondary structures of riboswitches can be accurately predicted once the ‘switching sequence’ of the riboswitch has been properly identified. The proposed SwiSpot approach is capable of identifying the switching sequence inside a putative, complete riboswitch sequence, on the basis of pairing behaviors, which are evaluated on proper sets of configurations. Moreover, it is able to model the switching behavior of riboswitches whose generated ensemble covers both alternate configurations. Beyond structural predictions, the approach can also be paired to homology-based riboswitch searches. Availability and Implementation: SwiSpot software, along with the reference dataset files, is available at: http://www.iet.unipi.it/a.bechini/swispot/ Supplementary information: Supplementary data are available at Bioinformatics online. Contact: a.bechini@ing.unipi.it |
Author | Novoa, Eva Maria Barsacchi, Marco Bechini, Alessio Kellis, Manolis |
Author_xml | – sequence: 1 givenname: Marco surname: Barsacchi fullname: Barsacchi, Marco organization: Department of Information Engineering, University of Pisa, Largo L. Lazzarino, Pisa, IT 56122, Italy – sequence: 2 givenname: Eva Maria surname: Novoa fullname: Novoa, Eva Maria organization: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA – sequence: 3 givenname: Manolis surname: Kellis fullname: Kellis, Manolis organization: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA – sequence: 4 givenname: Alessio surname: Bechini fullname: Bechini, Alessio organization: Department of Information Engineering, University of Pisa, Largo L. Lazzarino, Pisa, IT 56122, Italy |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/27378291$$D View this record in MEDLINE/PubMed |
BookMark | eNpVkMtOwzAQRS1URGnhE0BZsgn1K07CDipeUiUWhXVkO2MwSuJiO6r696RKqcRqZnTvzB2dGZp0rgOErgi-JbhkC2Wd7YzzrYxWh4WKW47JCTonTOQpLwiZHHvMpmgWwjfGOMOZOENTmrO8oCU5Rw_rrV1vXLxLWldDY7vPxFvlwtZG_QUhUbskDHLcC66PySjspwA_PXQawgU6NbIJcHmoc_Tx9Pi-fElXb8-vy_tVqjmlMdUgpNREDz-IkmsKGIgxGnLJajCFkFDkhmooOGQKl1LXteYm41yxAkgp2BzdjHc33g3RIVatDRqaRnbg-lCRgoqcEJyVgzUbrdq7EDyYauNtK_2uIrja46v-46tGfMPe9SGiVy3Ux60_XuwXIXh1YA |
CitedBy_id | crossref_primary_10_1042_BST20180507 crossref_primary_10_1021_acs_jctc_3c01239 crossref_primary_10_1016_j_disc_2021_112371 crossref_primary_10_1371_journal_pone_0217625 crossref_primary_10_1021_acsomega_9b01430 crossref_primary_10_1007_s10801_022_01132_3 crossref_primary_10_1080_17460441_2022_2134852 crossref_primary_10_1371_journal_pone_0241664 crossref_primary_10_2323_jgam_2018_08_001 |
Cites_doi | 10.1093/bioinformatics/btu649 10.1016/j.cell.2009.01.043 10.1093/bioinformatics/btp157 10.1371/journal.pcbi.1002368 10.1093/bioinformatics/bth129 10.1016/0377-0427(87)90125-7 10.1093/nar/gki445 10.1186/s12859-015-0523-2 10.1186/1471-2105-13-S5-S6 10.1101/cshperspect.a003533 10.1101/cshperspect.a003566 10.1186/1748-7188-6-26 10.1093/molbev/mst010 10.1093/bioinformatics/btm314 10.1093/nar/22.23.4953 10.1126/science.1151298 10.1002/bip.360290621 10.1145/2851613.2851868 10.1016/j.febslet.2012.02.038 10.1093/nar/gkg938 10.1093/nar/gku1063 10.1261/rna.1623809 10.1016/j.cell.2012.12.024 10.1016/j.bbagrm.2014.02.012 10.1073/pnas.0401799101 10.1073/pnas.92.19.8793 |
ContentType | Journal Article |
Copyright | The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com. |
Copyright_xml | – notice: The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com. |
DBID | CGR CUY CVF ECM EIF NPM AAYXX CITATION 7X8 |
DOI | 10.1093/bioinformatics/btw401 |
DatabaseName | Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed CrossRef MEDLINE - Academic |
DatabaseTitle | MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) CrossRef MEDLINE - Academic |
DatabaseTitleList | MEDLINE MEDLINE - Academic CrossRef |
Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: EIF name: MEDLINE url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search sourceTypes: Index Database |
DeliveryMethod | fulltext_linktorsrc |
Discipline | Biology |
EISSN | 1367-4811 |
EndPage | 3259 |
ExternalDocumentID | 10_1093_bioinformatics_btw401 27378291 |
Genre | Research Support, Non-U.S. Gov't Journal Article |
GroupedDBID | --- -E4 -~X .2P .DC .I3 0R~ 1TH 23N 2WC 4.4 48X 53G 5GY 5WA 70D AAIJN AAIMJ AAJKP AAJQQ AAKPC AAMDB AAMVS AAOGV AAPQZ AAPXW AAUQX AAVAP AAVLN ABEUO ABIXL ABNKS ABPTD ABQLI ABWST ABXVV ABZBJ ACGFS ACIWK ACPRK ACUFI ACYTK ADBBV ADEYI ADEZT ADFTL ADGKP ADGZP ADHKW ADHZD ADOCK ADPDF ADRDM ADRIX ADRTK ADVEK ADYVW ADZTZ ADZXQ AECKG AEGPL AEJOX AEKKA AEKSI AELWJ AEMDU AENEX AENZO AEPUE AETBJ AEWNT AFFZL AFGWE AFIYH AFOFC AFRAH AFXEN AGINJ AGKEF AGQXC AGSYK AHMBA AHXPO AIJHB AJEEA AJEUX AKHUL AKWXX ALMA_UNASSIGNED_HOLDINGS ALTZX ALUQC APIBT APWMN ARIXL ASPBG AVWKF AXUDD AYOIW AZVOD BAWUL BAYMD BCRHZ BHONS BQDIO BQUQU BSWAC BTQHN C45 CDBKE CGR CS3 CUY CVF CZ4 DAKXR DIK DILTD DU5 D~K EBD EBS ECM EE~ EIF EJD EMOBN F5P F9B FEDTE FHSFR FLIZI FLUFQ FOEOM FQBLK GAUVT GJXCC GX1 H13 H5~ HAR HW0 HZ~ IOX J21 JXSIZ KAQDR KOP KQ8 KSI KSN M-Z M49 MK~ ML0 N9A NGC NLBLG NMDNZ NOMLY NPM NU- NVLIB O9- OAWHX ODMLO OJQWA OK1 OVD OVEED P2P PAFKI PEELM PQQKQ Q1. Q5Y R44 RD5 RIG RNS ROL ROX RPM RUSNO RW1 RXO SV3 TEORI TJP TLC TOX TR2 W8F WOQ X7H YAYTL YKOAZ YXANX ZKX ~91 ~KM AAYXX ABEJV CITATION GROUPED_DOAJ 7X8 |
ID | FETCH-LOGICAL-c422t-ce6aac1c050694c2e0e1ffce7a3def86ae87f2ce84e5b09acddc4f544b38e1963 |
ISSN | 1367-4803 |
IngestDate | Tue Dec 03 23:40:13 EST 2024 Fri Dec 06 04:00:59 EST 2024 Wed Oct 16 00:57:32 EDT 2024 |
IsDoiOpenAccess | false |
IsOpenAccess | true |
IsPeerReviewed | true |
IsScholarly | true |
Issue | 21 |
Language | English |
License | The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com. |
LinkModel | OpenURL |
MergedId | FETCHMERGED-LOGICAL-c422t-ce6aac1c050694c2e0e1ffce7a3def86ae87f2ce84e5b09acddc4f544b38e1963 |
Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
OpenAccessLink | https://academic.oup.com/bioinformatics/article-pdf/32/21/3252/7889653/btw401.pdf |
PMID | 27378291 |
PQID | 1826711059 |
PQPubID | 23479 |
PageCount | 8 |
ParticipantIDs | proquest_miscellaneous_1826711059 crossref_primary_10_1093_bioinformatics_btw401 pubmed_primary_27378291 |
PublicationCentury | 2000 |
PublicationDate | 2016-11-01 |
PublicationDateYYYYMMDD | 2016-11-01 |
PublicationDate_xml | – month: 11 year: 2016 text: 2016-11-01 day: 01 |
PublicationDecade | 2010 |
PublicationPlace | England |
PublicationPlace_xml | – name: England |
PublicationTitle | Bioinformatics (Oxford, England) |
PublicationTitleAlternate | Bioinformatics |
PublicationYear | 2016 |
References | Gruber (2023020113513877100_btw401-B12) 2010 Voss (2023020113513877100_btw401-B26) 2004; 20 Chang (2023020113513877100_btw401-B4) 2009; 15 Wittmann (2023020113513877100_btw401-B29) 2012; 586 Rousseeuw (2023020113513877100_btw401-B24) 1987; 20 Clote (2023020113513877100_btw401-B6) 2015 Lorenz (2023020113513877100_btw401-B15) 2011; 6 Serganov (2023020113513877100_btw401-B25) 2013; 152 Wilson (2023020113513877100_btw401-B28) 1995; 92 Katoh (2023020113513877100_btw401-B14) 2013; 30 Peselis (2023020113513877100_btw401-B22) 2014; 1839 Nawrocki (2023020113513877100_btw401-B20) 2009; 25 Abreu-Goodger (2023020113513877100_btw401-B1) 2005; 33 (Suppl 2) Freyhult (2023020113513877100_btw401-B9) 2007; 23 Barsacchi (2023020113513877100_btw401-B2) 2016 Clote (2023020113513877100_btw401-B7) 2012; 13 Chen (2023020113513877100_btw401-B5) 1994; 22 Nawrocki (2023020113513877100_btw401-B21) 2015; 43 Breaker (2023020113513877100_btw401-B3) 2012; 4 McCaskill (2023020113513877100_btw401-B19) 1990; 29 Manzourolajdad (2023020113513877100_btw401-B17) 2015; 16 Ding (2023020113513877100_btw401-B8) 2003; 31 Greenleaf (2023020113513877100_btw401-B11) 2008; 319 Janssen (2023020113513877100_btw401-B13) 2014; 31 Waters (2023020113513877100_btw401-B27) 2009; 136 Quarta (2023020113513877100_btw401-B23) 2012; 8 Garst (2023020113513877100_btw401-B10) 2011; 3 Lünse (2023020113513877100_btw401-B16) 2014; 304 Mathews (2023020113513877100_btw401-B18) 2004; 101 |
References_xml | – volume: 31 start-page: 423 year: 2014 ident: 2023020113513877100_btw401-B13 article-title: The RNA shapes studio publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu649 contributor: fullname: Janssen – volume: 136 start-page: 615 year: 2009 ident: 2023020113513877100_btw401-B27 article-title: Regulatory RNAs in bacteria publication-title: Cell doi: 10.1016/j.cell.2009.01.043 contributor: fullname: Waters – volume: 25 start-page: 1335 year: 2009 ident: 2023020113513877100_btw401-B20 article-title: Infernal 1.0: inference of RNA alignments publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp157 contributor: fullname: Nawrocki – volume: 8 start-page: e1002368. year: 2012 ident: 2023020113513877100_btw401-B23 article-title: Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function publication-title: PloS Comput. Biol doi: 10.1371/journal.pcbi.1002368 contributor: fullname: Quarta – volume: 20 start-page: 1573 year: 2004 ident: 2023020113513877100_btw401-B26 article-title: Evaluating the predictability of conformational switching in RNA publication-title: Bioinformatics doi: 10.1093/bioinformatics/bth129 contributor: fullname: Voss – volume: 20 start-page: 53 year: 1987 ident: 2023020113513877100_btw401-B24 article-title: Silhouettes: A graphical aid to the interpretation and validation of cluster analysis publication-title: J. Comput. Appl. Math doi: 10.1016/0377-0427(87)90125-7 contributor: fullname: Rousseeuw – volume: 33 (Suppl 2) start-page: W690 year: 2005 ident: 2023020113513877100_btw401-B1 article-title: RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements publication-title: Nucleic Acids Res doi: 10.1093/nar/gki445 contributor: fullname: Abreu-Goodger – volume: 16 start-page: 133. year: 2015 ident: 2023020113513877100_btw401-B17 article-title: Secondary structural entropy in RNA switch (riboswitch) identification publication-title: BMC Bioinformatics doi: 10.1186/s12859-015-0523-2 contributor: fullname: Manzourolajdad – volume: 13 start-page: 1 year: 2012 ident: 2023020113513877100_btw401-B7 article-title: Maximum expected accuracy structural neighbors of an RNA secondary structure publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-13-S5-S6 contributor: fullname: Clote – volume: 3 year: 2011 ident: 2023020113513877100_btw401-B10 article-title: Riboswitches: structures and mechanisms publication-title: Cold Spring Harb. Perspect. Biol doi: 10.1101/cshperspect.a003533 contributor: fullname: Garst – volume: 4 year: 2012 ident: 2023020113513877100_btw401-B3 article-title: Riboswitches and the RNA world publication-title: Cold Spring Harb. Perspect. Biol doi: 10.1101/cshperspect.a003566 contributor: fullname: Breaker – volume: 6 start-page: 26 year: 2011 ident: 2023020113513877100_btw401-B15 article-title: ViennaRNA package 2.0 publication-title: Algorithm Mol. Biol doi: 10.1186/1748-7188-6-26 contributor: fullname: Lorenz – year: 2010 ident: 2023020113513877100_btw401-B12 contributor: fullname: Gruber – volume: 30 start-page: 772 year: 2013 ident: 2023020113513877100_btw401-B14 article-title: Mafft multiple sequence alignment software version 7: Improvements in performance and usability publication-title: Mol. Biol. Evol doi: 10.1093/molbev/mst010 contributor: fullname: Katoh – volume: 23 start-page: 2054 year: 2007 ident: 2023020113513877100_btw401-B9 article-title: Boltzmann probability of RNA structural neighbors and riboswitch detection publication-title: Bioinformatics doi: 10.1093/bioinformatics/btm314 contributor: fullname: Freyhult – volume: 304 start-page: 79 year: 2014 ident: 2023020113513877100_btw401-B16 article-title: The promise of riboswitches as potential antibacterial drug targets publication-title: Ijmm contributor: fullname: Lünse – volume: 22 start-page: 4953 year: 1994 ident: 2023020113513877100_btw401-B5 article-title: Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs publication-title: Nucleic Acids Res doi: 10.1093/nar/22.23.4953 contributor: fullname: Chen – volume-title: Computational Methods for Understanding Riboswitches, volume 553 of Methods in Enzymology year: 2015 ident: 2023020113513877100_btw401-B6 contributor: fullname: Clote – volume: 319 start-page: 630 year: 2008 ident: 2023020113513877100_btw401-B11 article-title: Direct observation of hierarchical folding in single riboswitch aptamers publication-title: Science doi: 10.1126/science.1151298 contributor: fullname: Greenleaf – volume: 29 start-page: 1105 year: 1990 ident: 2023020113513877100_btw401-B19 article-title: The equilibrium partition function and base pair binding probabilities for RNA secondary structure publication-title: Biopolymers doi: 10.1002/bip.360290621 contributor: fullname: McCaskill – start-page: 44 volume-title: Proc. of 31st ACM Symp. on Applied Computing year: 2016 ident: 2023020113513877100_btw401-B2 doi: 10.1145/2851613.2851868 contributor: fullname: Barsacchi – volume: 586 start-page: 2076 year: 2012 ident: 2023020113513877100_btw401-B29 article-title: Engineered riboswitches: Expanding researchers' toolbox with synthetic RNA regulators publication-title: FEBS Letters doi: 10.1016/j.febslet.2012.02.038 contributor: fullname: Wittmann – volume: 31 start-page: 7280 year: 2003 ident: 2023020113513877100_btw401-B8 article-title: A statistical sampling algorithm for RNA secondary structure prediction publication-title: Nucleic Acids Res doi: 10.1093/nar/gkg938 contributor: fullname: Ding – volume: 43 start-page: D130 year: 2015 ident: 2023020113513877100_btw401-B21 article-title: Rfam 12.0: updates to the RNA families database publication-title: Nucleic Acids Res doi: 10.1093/nar/gku1063 contributor: fullname: Nawrocki – volume: 15 start-page: 1426 year: 2009 ident: 2023020113513877100_btw401-B4 article-title: Computational identification of riboswitches based on RNA conserved functional sequences and conformations publication-title: RNA doi: 10.1261/rna.1623809 contributor: fullname: Chang – volume: 152 start-page: 17 year: 2013 ident: 2023020113513877100_btw401-B25 article-title: A decade of riboswitches publication-title: Cell doi: 10.1016/j.cell.2012.12.024 contributor: fullname: Serganov – volume: 1839 start-page: 908 year: 2014 ident: 2023020113513877100_btw401-B22 article-title: Themes and variations in riboswitch structure and function publication-title: Biochim. Biophys. Acta doi: 10.1016/j.bbagrm.2014.02.012 contributor: fullname: Peselis – volume: 101 start-page: 7287 year: 2004 ident: 2023020113513877100_btw401-B18 article-title: Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.0401799101 contributor: fullname: Mathews – volume: 92 start-page: 8793 year: 1995 ident: 2023020113513877100_btw401-B28 article-title: Transcription termination at intrinsic terminators: the role of the RNA hairpin publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.92.19.8793 contributor: fullname: Wilson |
SSID | ssj0005056 |
Score | 2.3339086 |
Snippet | Riboswitches are cis-regulatory elements in mRNA, mostly found in Bacteria, which exhibit two main secondary structure conformations. Although one of them... Motivation: Riboswitches are cis-regulatory elements in mRNA, mostly found in Bacteria, which exhibit two main secondary structure conformations. Although one... MOTIVATIONRiboswitches are cis-regulatory elements in mRNA, mostly found in Bacteria, which exhibit two main secondary structure conformations. Although one of... |
SourceID | proquest crossref pubmed |
SourceType | Aggregation Database Index Database |
StartPage | 3252 |
SubjectTerms | Bacteria Ligands Models, Genetic Riboswitch Sequence Analysis, RNA Software |
Title | SwiSpot: modeling riboswitches by spotting out switching sequences |
URI | https://www.ncbi.nlm.nih.gov/pubmed/27378291 https://search.proquest.com/docview/1826711059 |
Volume | 32 |
hasFullText | 1 |
inHoldings | 1 |
isFullTextHit | |
isPrint | |
link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3da9RAEF_OiuCL-N3ziwi-Sdpsdi-X-GZFKUL1oVe4t7C7mUCgJKWXeNb_xP_Wmd1NcpEq1peQbGCS7PwyOzM7H4y9yYQErrUIVZGIUBZooKTLMg7jQvM0KwQXNjbn5EtyfCY_rxfr2eznTtRS1-oD8-PavJL_4SqOIV8pS_YGnB2I4gCeI3_xiBzG4z_x-HRbnV401rlnO9qQ2X9Z6WazrYgZG9It0Wz1oc1d-9bdsC6EPoR6sqtbNb6Qqi3eTJVIv_fB777bx47n4AhtYmWM7QpMOT-mGTzLzbfGKqWop9OdSo1y_dw3YD9RdXNejU56oPeqfM4Nhebu-iN44hPzRhEqqJJ6GjmxBbtjXqx6uTv6Nbs-TdpLURG7qrZ-RcbL7Fpp7yph6cnc0EC7lf6NJvW1f1v3hmhEtw8v8imh3JG5xW5TjUVqy7D6uh6jhyLbGHj42D45LBOHUzKHjsxU7fmDLWN1mtV9ds8bI8F7h6wHbAb1Q3bHtSe9esSOPL7eBT26gl10Bfoq6NEVILqCAV3BgK7H7OzTx9WH49D33AiNjOM2NJAoZbjBD0wyaWKIgJelgaUSBZRpooB-ZQOphIWOMmWKwshyIaUWKZA0f8L26qaGfRZoEFSsjqclGCkjlXJRlJABrmgZh0jM2UE_JfmFK62S_5UVc_a6n7gchSDtbKkamm6Tk5G85GQqzNlTN6MDSdTPUQvO-LObPu45uzvi-wXbay87eIkaaKtfWSz8AuafkAQ |
link.rule.ids | 314,780,784,27924,27925 |
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=SwiSpot%3A+modeling+riboswitches+by+spotting+out+switching+sequences&rft.jtitle=Bioinformatics+%28Oxford%2C+England%29&rft.au=Barsacchi%2C+Marco&rft.au=Novoa%2C+Eva+Maria&rft.au=Kellis%2C+Manolis&rft.au=Bechini%2C+Alessio&rft.date=2016-11-01&rft.issn=1367-4803&rft.eissn=1367-4811&rft.volume=32&rft.issue=21&rft.spage=3252&rft.epage=3259&rft_id=info:doi/10.1093%2Fbioinformatics%2Fbtw401&rft.externalDBID=n%2Fa&rft.externalDocID=10_1093_bioinformatics_btw401 |
thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1367-4803&client=summon |
thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1367-4803&client=summon |
thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1367-4803&client=summon |