MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing
Motivation: As more non–coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function of the molecule, programs for RNA structure prediction are necessary tools in this growing field of research. Furthermore, it is k...
Saved in:
| Published in | Bioinformatics Vol. 23; no. 24; pp. 3304 - 3311 |
|---|---|
| Main Authors | , , |
| Format | Journal Article |
| Language | English |
| Published |
Oxford
Oxford University Press
15.12.2007
Oxford Publishing Limited (England) |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1367-4803 1367-4811 1460-2059 1367-4811 |
| DOI | 10.1093/bioinformatics/btm525 |
Cover
| Abstract | Motivation: As more non–coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function of the molecule, programs for RNA structure prediction are necessary tools in this growing field of research. Furthermore, it is known that RNA structure is often evolutionarily more conserved than sequence. However, few existing methods are capable of simultaneously considering multiple sequence alignment and structure prediction. Result: We present a novel solution to the problem of simultaneous structure prediction and multiple alignment of RNA sequences. Using Markov chain Monte Carlo in a simulated annealing framework, the algorithm MASTR (Multiple Alignment of STructural RNAs) iteratively improves both sequence alignment and structure prediction for a set of RNA sequences. This is done by minimizing a combined cost function that considers sequence conservation, covariation and basepairing probabilities. The results show that the method is very competitive to similar programs available today, both in terms of accuracy and computational efficiency. Availability: Source code available from http://mastr.binf.ku.dk/ Contact: stinus@binf.ku.dk |
|---|---|
| AbstractList | Motivation: As more non–coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function of the molecule, programs for RNA structure prediction are necessary tools in this growing field of research. Furthermore, it is known that RNA structure is often evolutionarily more conserved than sequence. However, few existing methods are capable of simultaneously considering multiple sequence alignment and structure prediction. Result: We present a novel solution to the problem of simultaneous structure prediction and multiple alignment of RNA sequences. Using Markov chain Monte Carlo in a simulated annealing framework, the algorithm MASTR (Multiple Alignment of STructural RNAs) iteratively improves both sequence alignment and structure prediction for a set of RNA sequences. This is done by minimizing a combined cost function that considers sequence conservation, covariation and basepairing probabilities. The results show that the method is very competitive to similar programs available today, both in terms of accuracy and computational efficiency. Availability: Source code available from http://mastr.binf.ku.dk/ Contact: stinus@binf.ku.dk As more non-coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function of the molecule, programs for RNA structure prediction are necessary tools in this growing field of research. Furthermore, it is known that RNA structure is often evolutionarily more conserved than sequence. However, few existing methods are capable of simultaneously considering multiple sequence alignment and structure prediction.MOTIVATIONAs more non-coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function of the molecule, programs for RNA structure prediction are necessary tools in this growing field of research. Furthermore, it is known that RNA structure is often evolutionarily more conserved than sequence. However, few existing methods are capable of simultaneously considering multiple sequence alignment and structure prediction.We present a novel solution to the problem of simultaneous structure prediction and multiple alignment of RNA sequences. Using Markov chain Monte Carlo in a simulated annealing framework, the algorithm MASTR (Multiple Alignment of STructural RNAs) iteratively improves both sequence alignment and structure prediction for a set of RNA sequences. This is done by minimizing a combined cost function that considers sequence conservation, covariation and basepairing probabilities. The results show that the method is very competitive to similar programs available today, both in terms of accuracy and computational efficiency.RESULTWe present a novel solution to the problem of simultaneous structure prediction and multiple alignment of RNA sequences. Using Markov chain Monte Carlo in a simulated annealing framework, the algorithm MASTR (Multiple Alignment of STructural RNAs) iteratively improves both sequence alignment and structure prediction for a set of RNA sequences. This is done by minimizing a combined cost function that considers sequence conservation, covariation and basepairing probabilities. The results show that the method is very competitive to similar programs available today, both in terms of accuracy and computational efficiency.Source code available from http://mastr.binf.ku.dk/AVAILABILITYSource code available from http://mastr.binf.ku.dk/ Motivation: As more non–coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function of the molecule, programs for RNA structure prediction are necessary tools in this growing field of research. Furthermore, it is known that RNA structure is often evolutionarily more conserved than sequence. However, few existing methods are capable of simultaneously considering multiple sequence alignment and structure prediction. Result: We present a novel solution to the problem of simultaneous structure prediction and multiple alignment of RNA sequences. Using Markov chain Monte Carlo in a simulated annealing framework, the algorithm MASTR (Multiple Alignment of STructural RNAs) iteratively improves both sequence alignment and structure prediction for a set of RNA sequences. This is done by minimizing a combined cost function that considers sequence conservation, covariation and basepairing probabilities. The results show that the method is very competitive to similar programs available today, both in terms of accuracy and computational efficiency. Availability: Source code available from http://mastr.binf.ku.dk/ Contact: stinus@binf.ku.dk MOTIVATION: As more non-coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function of the molecule, programs for RNA structure prediction are necessary tools in this growing field of research. Furthermore, it is known that RNA structure is often evolutionarily more conserved than sequence. However, few existing methods are capable of simultaneously considering multiple sequence alignment and structure prediction. RESULT: We present a novel solution to the problem of simultaneous structure prediction and multiple alignment of RNA sequences. Using Markov chain Monte Carlo in a simulated annealing framework, the algorithm MASTR (Multiple Alignment of STructural RNAs) iteratively improves both sequence alignment and structure prediction for a set of RNA sequences. This is done by minimizing a combined cost function that considers sequence conservation, covariation and basepairing probabilities. The results show that the method is very competitive to similar programs available today, both in terms of accuracy and computational efficiency. As more non-coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function of the molecule, programs for RNA structure prediction are necessary tools in this growing field of research. Furthermore, it is known that RNA structure is often evolutionarily more conserved than sequence. However, few existing methods are capable of simultaneously considering multiple sequence alignment and structure prediction. We present a novel solution to the problem of simultaneous structure prediction and multiple alignment of RNA sequences. Using Markov chain Monte Carlo in a simulated annealing framework, the algorithm MASTR (Multiple Alignment of STructural RNAs) iteratively improves both sequence alignment and structure prediction for a set of RNA sequences. This is done by minimizing a combined cost function that considers sequence conservation, covariation and basepairing probabilities. The results show that the method is very competitive to similar programs available today, both in terms of accuracy and computational efficiency. Source code available from http://mastr.binf.ku.dk/ Motivation: As more non-coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function of the molecule, programs for RNA structure prediction are necessary tools in this growing field of research. Furthermore, it is known that RNA structure is often evolutionarily more conserved than sequence. However, few existing methods are capable of simultaneously considering multiple sequence alignment and structure prediction. Result: We present a novel solution to the problem of simultaneous structure prediction and multiple alignment of RNA sequences. Using Markov chain Monte Carlo in a simulated annealing framework, the algorithm MASTR (Multiple Alignment of STructural RNAs) iteratively improves both sequence alignment and structure prediction for a set of RNA sequences. This is done by minimizing a combined cost function that considers sequence conservation, covariation and basepairing probabilities. The results show that the method is very competitive to similar programs available today, both in terms of accuracy and computational efficiency. Availability: Source code available from http://mastr.binf.ku.dk/ Contact: stinus@binf.ku.dk |
| Author | Lindgreen, Stinus Krogh, Anders Gardner, Paul P. |
| Author_xml | – sequence: 1 givenname: Stinus surname: Lindgreen fullname: Lindgreen, Stinus organization: Bioinformatics Centre and Molecular Evolution Group, Department of Molecular Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark – sequence: 2 givenname: Paul P. surname: Gardner fullname: Gardner, Paul P. organization: Bioinformatics Centre and Molecular Evolution Group, Department of Molecular Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark – sequence: 3 givenname: Anders surname: Krogh fullname: Krogh, Anders organization: Bioinformatics Centre and Molecular Evolution Group, Department of Molecular Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=19906984$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/18006551$$D View this record in MEDLINE/PubMed |
| BookMark | eNqNkUtv1DAURiNURB_wE0AREt2F2uM3rEblMUgDiDJIFRvLcZyRS2IHP1T67_EoIyq6aVe-i3Ou7_3ucXXgvDNV9RyC1xAIdNZab13vw6iS1fGsTSNZkEfVEcQUNAtAxEGpEWUN5gAdVscxXgFAIMb4SXUIOQCUEHhUyc_L75uLN_WYh2SnwdRqsFs3Gpdq5bo6ppB1ysHUUzCd1cl6V_u-LsM02nfWbeuLL8tY57groy1tVDJdcZ0pndz2afW4V0M0z_bvSfXjw_vN-apZf_346Xy5bjThLDUMGQAEIZqzlikMSY970rG2Y0C1CGjFEe85oYwwQFoCeyEWCC1ghw3mbalPKjr3zW5SN9dqGOQU7KjCjYRA7hKT_ycm58SKeDqLU_C_s4lJjjZqMwzKGZ-jpAJgBuH9IBSUCcF2o7y8A175HFzZvjCcMo4ZKtCLPZTb0XS3w-4vU4BXe0BFrYY-KKdtvOWEAFRwXDgyczr4GIPpH7z32zuetknt7puCssO9Nphtn6cHf9jMio3J_PknqfBLUoYYkavLn_LderO6XG028hv6C5b86-w |
| CODEN | BOINFP |
| CitedBy_id | crossref_primary_10_1142_S0219720018500154 crossref_primary_10_1093_nar_gkac844 crossref_primary_10_1093_bioinformatics_btn495 crossref_primary_10_1016_j_swevo_2017_02_002 crossref_primary_10_1007_s12065_018_00198_y crossref_primary_10_3390_molecules26154420 crossref_primary_10_1093_nar_gkn275 crossref_primary_10_1142_S0219720010004549 crossref_primary_10_1093_bioinformatics_btq726 crossref_primary_10_1371_journal_pone_0152238 crossref_primary_10_1093_bioinformatics_btn177 crossref_primary_10_1261_rna_073015_119 crossref_primary_10_1093_bfgp_elp043 crossref_primary_10_1007_s10142_022_00947_4 crossref_primary_10_1080_00268976_2014_885611 crossref_primary_10_1155_2017_9139504 crossref_primary_10_1016_j_bbrc_2012_03_014 crossref_primary_10_1093_nar_gkp600 crossref_primary_10_1002_cpbi_4 crossref_primary_10_1186_1471_2105_12_108 crossref_primary_10_1007_s00299_017_2210_4 crossref_primary_10_1186_1471_2105_12_S1_S38 crossref_primary_10_1093_bioinformatics_btr421 crossref_primary_10_1186_1471_2105_9_212 crossref_primary_10_1021_acsptsci_3c00388 crossref_primary_10_1093_nar_gkr244 crossref_primary_10_1093_bib_bbaa354 crossref_primary_10_1093_nar_gkr1081 crossref_primary_10_1142_S0218126617500669 crossref_primary_10_1186_1471_2105_14_118 crossref_primary_10_1093_bib_bbad421 crossref_primary_10_1093_bioinformatics_btp580 crossref_primary_10_1261_rna_1617009 crossref_primary_10_1186_s12944_018_0915_1 crossref_primary_10_1007_s12033_008_9114_z crossref_primary_10_1093_bioinformatics_btq439 crossref_primary_10_3390_ijms140815423 crossref_primary_10_1371_journal_pcbi_1012446 crossref_primary_10_1016_j_compbiolchem_2015_02_002 crossref_primary_10_1016_j_physa_2010_02_015 crossref_primary_10_1093_bib_bbv099 crossref_primary_10_1093_bioinformatics_bts612 crossref_primary_10_1080_00268976_2013_775515 crossref_primary_10_1371_journal_pcbi_1009461 crossref_primary_10_3724_SP_J_1206_2009_00047 crossref_primary_10_1016_j_bbrc_2018_12_042 |
| Cites_doi | 10.1093/nar/22.22.4673 10.1038/nbt1144 10.1016/j.sbi.2004.04.001 10.1093/bioinformatics/bti577 10.1137/0218082 10.1093/bioinformatics/bth229 10.1017/CBO9780511790492 10.1093/bioinformatics/btm049 10.1093/bioinformatics/btl514 10.1016/S0022-2836(02)00308-X 10.1093/nar/25.18.3724 10.1093/nar/gki081 10.1016/j.thbio.2005.01.002 10.1093/nar/27.13.2682 10.1093/nar/gkg599 10.1093/nar/gkg614 10.1093/nar/9.1.133 10.1126/science.1108625 10.1137/0135006 10.1093/biomet/57.1.97 10.1093/bioinformatics/bti550 10.1137/0145048 10.1073/pnas.0703836104 10.1016/j.mib.2007.05.010 10.1006/jmbi.2001.5351 10.1126/science.220.4598.671 10.1093/nar/gkg938 10.1093/nar/gki541 10.1017/CBO9780511613586 10.1093/bioinformatics/btm272 10.1093/nar/20.10.2511 10.1371/journal.pcbi.0020033 10.1016/j.sbi.2007.03.001 10.1093/nar/gkh779 10.1145/322139.322143 10.1371/journal.pcbi.0030149 10.1093/bioinformatics/15.6.446 10.1093/bioinformatics/bti279 10.1371/journal.pcbi.0030065 10.1002/bip.360290621 10.1093/bib/bbm011 |
| ContentType | Journal Article |
| Copyright | The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org 2007 2008 INIST-CNRS The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org |
| Copyright_xml | – notice: The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org 2007 – notice: 2008 INIST-CNRS – notice: The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org |
| DBID | BSCLL AAYXX CITATION IQODW CGR CUY CVF ECM EIF NPM 7QF 7QO 7QQ 7SC 7SE 7SP 7SR 7TA 7TB 7TM 7TO 7U5 8BQ 8FD F28 FR3 H8D H8G H94 JG9 JQ2 K9. KR7 L7M L~C L~D P64 7X8 ADTOC UNPAY |
| DOI | 10.1093/bioinformatics/btm525 |
| DatabaseName | Istex CrossRef Pascal-Francis Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed Aluminium Industry Abstracts Biotechnology Research Abstracts Ceramic Abstracts Computer and Information Systems Abstracts Corrosion Abstracts Electronics & Communications Abstracts Engineered Materials Abstracts Materials Business File Mechanical & Transportation Engineering Abstracts Nucleic Acids Abstracts Oncogenes and Growth Factors Abstracts Solid State and Superconductivity Abstracts METADEX Technology Research Database ANTE: Abstracts in New Technology & Engineering Engineering Research Database Aerospace Database Copper Technical Reference Library AIDS and Cancer Research Abstracts Materials Research Database ProQuest Computer Science Collection ProQuest Health & Medical Complete (Alumni) Civil Engineering Abstracts Advanced Technologies Database with Aerospace Computer and Information Systems Abstracts Academic Computer and Information Systems Abstracts Professional Biotechnology and BioEngineering Abstracts MEDLINE - Academic Unpaywall for CDI: Periodical Content Unpaywall |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) Materials Research Database Oncogenes and Growth Factors Abstracts Technology Research Database Computer and Information Systems Abstracts – Academic Mechanical & Transportation Engineering Abstracts Nucleic Acids Abstracts ProQuest Computer Science Collection Computer and Information Systems Abstracts ProQuest Health & Medical Complete (Alumni) Materials Business File Aerospace Database Copper Technical Reference Library Engineered Materials Abstracts Biotechnology Research Abstracts AIDS and Cancer Research Abstracts Advanced Technologies Database with Aerospace ANTE: Abstracts in New Technology & Engineering Civil Engineering Abstracts Aluminium Industry Abstracts Electronics & Communications Abstracts Ceramic Abstracts METADEX Biotechnology and BioEngineering Abstracts Computer and Information Systems Abstracts Professional Solid State and Superconductivity Abstracts Engineering Research Database Corrosion Abstracts MEDLINE - Academic |
| DatabaseTitleList | MEDLINE - Academic CrossRef Engineering Research Database MEDLINE Materials Research Database |
| 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 – sequence: 3 dbid: UNPAY name: Unpaywall url: https://proxy.k.utb.cz/login?url=https://unpaywall.org/ sourceTypes: Open Access Repository |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1460-2059 1367-4811 |
| EndPage | 3311 |
| ExternalDocumentID | 10.1093/bioinformatics/btm525 1398105261 18006551 19906984 10_1093_bioinformatics_btm525 ark_67375_HXZ_DLTHXHTT_Q |
| Genre | Research Support, Non-U.S. Gov't Journal Article |
| GroupedDBID | -~X .2P .I3 482 48X 5GY AAMVS ABGNP ABJNI ABPTD ACGFS ACUFI ADZXQ ALMA_UNASSIGNED_HOLDINGS BSCLL CZ4 EE~ F5P F9B H5~ HAR HW0 IOX KSI KSN NGC Q5Y RD5 ROZ RXO TLC TN5 TOX WH7 ~91 ADRIX BCRHZ KOP ROX --- -E4 .DC 0R~ 1TH 23N 2WC 4.4 53G 5WA 70D AAIJN AAIMJ AAJKP AAJQQ AAKPC AAMDB AAOGV AAPQZ AAPXW AAUQX AAVAP AAVLN AAYXX ABEJV ABEUO ABIXL ABNGD ABNKS ABPQP ABQLI ABWST ABXVV ABZBJ ACIWK ACPRK ACUKT ACUXJ ACYTK ADBBV ADEYI ADEZT ADFTL ADGKP ADGZP ADHKW ADHZD ADMLS ADOCK ADPDF ADRDM ADRTK ADVEK ADYVW ADZTZ AECKG AEGPL AEJOX AEKKA AEKSI AELWJ AEMDU AENEX AENZO AEPUE AETBJ AEWNT AFFNX AFFZL AFGWE AFIYH AFOFC AFRAH AGINJ AGKEF AGQPQ AGQXC AGSYK AHMBA AHXPO AIJHB AJEEA AJEUX AKHUL AKWXX ALTZX ALUQC AMNDL APIBT APWMN ARIXL ASPBG AVWKF AXUDD AYOIW AZFZN AZVOD BAWUL BAYMD BHONS BQDIO BQUQU BSWAC BTQHN C1A C45 CAG CDBKE CITATION COF CS3 DAKXR DIK DILTD DU5 D~K EBD EBS EJD EMOBN FEDTE FHSFR FLIZI FLUFQ FOEOM FQBLK GAUVT GJXCC GROUPED_DOAJ GX1 H13 HVGLF HZ~ J21 JXSIZ KAQDR KQ8 M-Z MK~ ML0 N9A NLBLG NMDNZ NOMLY NTWIH NU- NVLIB O0~ O9- OAWHX ODMLO OJQWA OK1 OVD OVEED P2P PAFKI PB- PEELM PQQKQ Q1. R44 RNS ROL RPM RUSNO RW1 SV3 TEORI TJP TR2 W8F WOQ X7H YAYTL YKOAZ YXANX ZKX ~KM .-4 .GJ ABEFU AI. AQDSO ATTQO ELUNK IQODW O~Y RIG RNI RZF RZO VH1 ZGI ABQTQ AFXEN CGR CUY CVF ECM EIF M49 NPM 7QF 7QO 7QQ 7SC 7SE 7SP 7SR 7TA 7TB 7TM 7TO 7U5 8BQ 8FD F28 FR3 H8D H8G H94 JG9 JQ2 K9. KR7 L7M L~C L~D P64 7X8 ADTOC UNPAY |
| ID | FETCH-LOGICAL-c587t-73e00955c87b7a415f4f5d7bd70ab30ca838f85675705b51f9923321d4e48b923 |
| IEDL.DBID | UNPAY |
| ISSN | 1367-4803 1367-4811 |
| IngestDate | Tue Aug 19 18:53:10 EDT 2025 Fri Sep 05 14:14:31 EDT 2025 Tue Oct 07 09:28:11 EDT 2025 Fri Oct 03 10:51:57 EDT 2025 Wed Feb 19 01:47:35 EST 2025 Mon Jul 21 09:13:52 EDT 2025 Wed Oct 01 04:04:43 EDT 2025 Thu Apr 24 23:06:38 EDT 2025 Wed Aug 28 03:24:15 EDT 2024 Sat Sep 20 11:01:51 EDT 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 24 |
| Keywords | Multiple RNA Structure Bioinformatics Prediction |
| Language | English |
| License | CC BY 4.0 |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c587t-73e00955c87b7a415f4f5d7bd70ab30ca838f85675705b51f9923321d4e48b923 |
| Notes | Associate Editor: Dmitrij Frishman To whom correspondence should be addressed. istex:F78F23EFC5F1314E80B76083FEC53DEC8A5BC363 ark:/67375/HXZ-DLTHXHTT-Q ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 |
| OpenAccessLink | https://proxy.k.utb.cz/login?url=https://academic.oup.com/bioinformatics/article-pdf/23/24/3304/49823971/bioinformatics_23_24_3304.pdf |
| PMID | 18006551 |
| PQID | 198678473 |
| PQPubID | 36124 |
| PageCount | 8 |
| ParticipantIDs | unpaywall_primary_10_1093_bioinformatics_btm525 proquest_miscellaneous_69047115 proquest_miscellaneous_19679972 proquest_journals_198678473 pubmed_primary_18006551 pascalfrancis_primary_19906984 crossref_primary_10_1093_bioinformatics_btm525 crossref_citationtrail_10_1093_bioinformatics_btm525 oup_primary_10_1093_bioinformatics_btm525 istex_primary_ark_67375_HXZ_DLTHXHTT_Q |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2007-12-15 |
| PublicationDateYYYYMMDD | 2007-12-15 |
| PublicationDate_xml | – month: 12 year: 2007 text: 2007-12-15 day: 15 |
| PublicationDecade | 2000 |
| PublicationPlace | Oxford |
| PublicationPlace_xml | – name: Oxford – name: England |
| PublicationTitle | Bioinformatics |
| PublicationTitleAlternate | Bioinformatics |
| PublicationYear | 2007 |
| Publisher | Oxford University Press Oxford Publishing Limited (England) |
| Publisher_xml | – name: Oxford University Press – name: Oxford Publishing Limited (England) |
| References | Athanasius (2023041107274143800_) 2007; 308 Tai (2023041107274143800_) 1979; 26 Zhang (2023041107274143800_) 1989; 18 Xu (2023041107274143800_) 2007; 23 Cheng (2023041107274143800_) 2005; 308 Giegerich (2023041107274143800_) 2004; 32 Gorodkin (2023041107274143800_) 1997; 25 Meyer (2023041107274143800_) 2007; 3 Hofacker (2023041107274143800_) 2004; 20 Havgaard (2023041107274143800_) 2005; 21 Reeder (2023041107274143800_) 2005; 21 Torarinsson (2023041107274143800_) 2007; 23 Hofacker (2023041107274143800_) 2003; 31 Nussinov (2023041107274143800_) 1978; 35 Hein (2023041107274143800_) 1989; 6 Thompson (2023041107274143800_) 1999; 27 Griffiths-Jones (2023041107274143800_) 2005; 33 Sankoff (2023041107274143800_) 1985; 45 Das (2023041107274143800_) 2007; 104 Bompfünewerer (2023041107274143800_) 2005; 123 Meyer (2023041107274143800_) 2007 Mathews (2023041107274143800_) 2002; 317 Zuker (2023041107274143800_) 1981; 9 Knudsen (2023041107274143800_) 1999; 15 Durbin (2023041107274143800_) 1998 Washietl (2023041107274143800_) 2005; 23 Lukashin (2023041107274143800_) 1992; 20 Pedersen (2023041107274143800_) 2006; 2 Häggström (2023041107274143800_) 2002 Siebert (2023041107274143800_) 2005; 21 McCaskill (2023041107274143800_) 1990; 29 Shapiro (2023041107274143800_) 2007; 17 Ding (2023041107274143800_) 2003; 31 Thompson (2023041107274143800_) 1994; 22 Lindgreen (2023041107274143800_) 2006; 22 Hastings (2023041107274143800_) 1970; 57 Höchsmann (2023041107274143800_) 2003 Jossinet (2023041107274143800_) 2007; 10 Hofacker (2023041107274143800_) 2002; 319 Onoa (2023041107274143800_) 2004; 14 Knudsen (2023041107274143800_) 2003; 31 Kirkpatrick (2023041107274143800_) 1983; 220 Gardner (2023041107274143800_) 2005; 33 Will (2023041107274143800_) 2007; 3 |
| References_xml | – volume: 22 start-page: 4673 year: 1994 ident: 2023041107274143800_ article-title: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice publication-title: Nucleic Acids Res doi: 10.1093/nar/22.22.4673 – volume: 23 start-page: 1383 year: 2005 ident: 2023041107274143800_ article-title: Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome publication-title: Nat. Biotechnol doi: 10.1038/nbt1144 – volume: 6 start-page: 649 year: 1989 ident: 2023041107274143800_ article-title: A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences when the phylogeny is given publication-title: Mol. Biol. Evol – volume: 14 start-page: 374 year: 2004 ident: 2023041107274143800_ article-title: RNA folding and unfolding publication-title: Curr. Opin. Struct. Biol doi: 10.1016/j.sbi.2004.04.001 – volume: 21 start-page: 3516 year: 2005 ident: 2023041107274143800_ article-title: Consensus shapes: An alternative to the Sankoff algorithm for RNA consensus structure prediction publication-title: Bioinformatics doi: 10.1093/bioinformatics/bti577 – volume: 18 start-page: 1245 year: 1989 ident: 2023041107274143800_ article-title: Simple fast algorithms for the editing distance between trees and related problems publication-title: SIAM J. Comput doi: 10.1137/0218082 – volume: 20 start-page: 2222 year: 2004 ident: 2023041107274143800_ article-title: Alignment of RNA base pairing probability matrices publication-title: Bioinformatics doi: 10.1093/bioinformatics/bth229 – volume-title: Biological Sequence Analysis. Probabilistic Models of Proteins and Nucleic Acids year: 1998 ident: 2023041107274143800_ doi: 10.1017/CBO9780511790492 – volume: 23 start-page: 926 year: 2007 ident: 2023041107274143800_ article-title: Multiple structural alignment and clustering of RNA sequences publication-title: Bioinformatics doi: 10.1093/bioinformatics/btm049 – volume: 22 start-page: 2988 year: 2006 ident: 2023041107274143800_ article-title: Measuring covariation in RNA alignments: physical realism improves information measures publication-title: Bioinformatics doi: 10.1093/bioinformatics/btl514 – volume: 319 start-page: 1059 year: 2002 ident: 2023041107274143800_ article-title: Secondary structure prediction for aligned RNA sequences publication-title: J. Mol. Biol doi: 10.1016/S0022-2836(02)00308-X – volume: 25 start-page: 3724 year: 1997 ident: 2023041107274143800_ article-title: Finding the most significant common sequence and structure motifs in a set of RNA sequences publication-title: Nucleic Acids Res doi: 10.1093/nar/25.18.3724 – volume: 33 start-page: D121 year: 2005 ident: 2023041107274143800_ article-title: Rfam: annotating non-coding RNAs in complete genomes publication-title: Nucleic Acids Res doi: 10.1093/nar/gki081 – volume: 123 start-page: 301 year: 2005 ident: 2023041107274143800_ article-title: Evolutionary patterns of non-coding RNAs publication-title: Theory Biosci doi: 10.1016/j.thbio.2005.01.002 – volume: 27 start-page: 2682 year: 1999 ident: 2023041107274143800_ article-title: A comprehensive comparison of multiple sequence alignment programs publication-title: Nucleic Acids Res doi: 10.1093/nar/27.13.2682 – volume: 31 start-page: 3429 year: 2003 ident: 2023041107274143800_ article-title: Vienna RNA secondary structure server publication-title: Nucleic Acids Res doi: 10.1093/nar/gkg599 – volume: 31 start-page: 3423 year: 2003 ident: 2023041107274143800_ article-title: Pfold: RNA secondary structure prediction using stochastic context-free grammars publication-title: Nucleic Acids Res doi: 10.1093/nar/gkg614 – volume: 9 start-page: 133 year: 1981 ident: 2023041107274143800_ article-title: Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information publication-title: Nucleic Acids Res doi: 10.1093/nar/9.1.133 – volume: 308 start-page: 1 year: 2007 ident: 2023041107274143800_ article-title: RNAs everywhere: genome-wide annotation of structured RNAs publication-title: J. Exp. Zoolog. Mol. Dev. Evol – volume: 308 start-page: 1149 year: 2005 ident: 2023041107274143800_ article-title: Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution publication-title: Science doi: 10.1126/science.1108625 – volume: 35 start-page: 68 year: 1978 ident: 2023041107274143800_ article-title: Algorithms for loop matchings publication-title: SIAM J. Appl. Math doi: 10.1137/0135006 – volume: 57 start-page: 97 year: 1970 ident: 2023041107274143800_ article-title: Monte carlo sampling methods using Markov chains and their applications publication-title: Biometrika doi: 10.1093/biomet/57.1.97 – volume: 21 start-page: 3352 year: 2005 ident: 2023041107274143800_ article-title: MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons publication-title: Bioinformatics doi: 10.1093/bioinformatics/bti550 – volume: 45 start-page: 810 year: 1985 ident: 2023041107274143800_ article-title: Simultaneous solution of the RNA folding, alignment and protosequence problems publication-title: SIAM J. Appl. Math doi: 10.1137/0145048 – volume: 104 start-page: 14664 year: 2007 ident: 2023041107274143800_ article-title: Automated de novo prediction of native-like RNA tertiary structures publication-title: Proc. Natl Acad. Sci doi: 10.1073/pnas.0703836104 – volume: 10 start-page: 279 year: 2007 ident: 2023041107274143800_ article-title: RNA structure: bioinformatic analysis publication-title: Curr. Opin. Microbiol doi: 10.1016/j.mib.2007.05.010 – volume: 317 start-page: 191 year: 2002 ident: 2023041107274143800_ article-title: Dynalign: an algorithm for finding the secondary structure common to two RNA sequences publication-title: J. Mol. Biol doi: 10.1006/jmbi.2001.5351 – volume: 220 start-page: 671 year: 1983 ident: 2023041107274143800_ article-title: Optimization by simulated annealing publication-title: Science doi: 10.1126/science.220.4598.671 – volume: 31 start-page: 7280 year: 2003 ident: 2023041107274143800_ article-title: A statistical sampling algorithm for RNA secondary structure prediction publication-title: Nucleic Acids Res doi: 10.1093/nar/gkg938 – volume: 33 start-page: 2433 year: 2005 ident: 2023041107274143800_ article-title: A benchmark of multiple sequence alignment programs upon structural RNAs publication-title: Nucleic Acids Res doi: 10.1093/nar/gki541 – volume-title: Finite Markov Chains and Algorithmic Applications year: 2002 ident: 2023041107274143800_ doi: 10.1017/CBO9780511613586 – volume: 23 start-page: 1883 year: 2007 ident: 2023041107274143800_ article-title: RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment publication-title: Bioinformatics doi: 10.1093/bioinformatics/btm272 – volume: 20 start-page: 2511 year: 1992 ident: 2023041107274143800_ article-title: Multiple alignment using simulated annealing: branch point definition in human mRNA splicing publication-title: Nucleic Acids Res doi: 10.1093/nar/20.10.2511 – volume: 2 start-page: e33 year: 2006 ident: 2023041107274143800_ article-title: Identification and classification of conserved RNA secondary structures in the human genome publication-title: PLoS Comput. Biol doi: 10.1371/journal.pcbi.0020033 – volume: 17 start-page: 157 year: 2007 ident: 2023041107274143800_ article-title: Bridging the gap in RNA structure prediction publication-title: Curr. Opin. Struct. Biol doi: 10.1016/j.sbi.2007.03.001 – volume: 32 start-page: 4843 year: 2004 ident: 2023041107274143800_ article-title: Abstract shapes of RNA publication-title: Nucleic Acids Res doi: 10.1093/nar/gkh779 – volume: 26 start-page: 422 year: 1979 ident: 2023041107274143800_ article-title: The tree-to-tree correction problem publication-title: J. ACM doi: 10.1145/322139.322143 – volume: 3 start-page: e149 year: 2007 ident: 2023041107274143800_ article-title: SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments and trees using a Bayesian MCMC framework publication-title: PLoS Comput. Biol doi: 10.1371/journal.pcbi.0030149 – volume: 15 start-page: 446 year: 1999 ident: 2023041107274143800_ article-title: RNA secondary structure prediction using stochastic context-free grammars and evolutionary history publication-title: Bioinformatics doi: 10.1093/bioinformatics/15.6.446 – volume: 21 start-page: 1815 year: 2005 ident: 2023041107274143800_ article-title: Pairwise local structure alignment of RNA sequences with sequence similarity less than 40% publication-title: Bioinformatics doi: 10.1093/bioinformatics/bti279 – volume: 3 start-page: e65 year: 2007 ident: 2023041107274143800_ article-title: Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering publication-title: PLoS Comput. Biol doi: 10.1371/journal.pcbi.0030065 – volume: 29 start-page: 1105 year: 1990 ident: 2023041107274143800_ article-title: The equilibrium partition function and base pair binding probabilities for RNA secondary structure publication-title: Biopolymers doi: 10.1002/bip.360290621 – year: 2007 ident: 2023041107274143800_ article-title: A practical guide to the art of RNA gene prediction publication-title: Brief. Bioinformatics doi: 10.1093/bib/bbm011 – start-page: 159 year: 2003 ident: 2023041107274143800_ article-title: Local similarity of RNA secondary structures |
| SSID | ssj0051444 ssj0005056 |
| Score | 2.1730783 |
| Snippet | Motivation: As more non–coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to... Motivation: As more non-coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to... As more non-coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function... MOTIVATION: As more non-coding RNAs are discovered, the importance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to... |
| SourceID | unpaywall proquest pubmed pascalfrancis crossref oup istex |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | 3304 |
| SubjectTerms | Algorithms Base Sequence Biological and medical sciences Fundamental and applied biological sciences. Psychology General aspects Markov chains Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Molecular Sequence Data RNA - genetics RNA, Untranslated - genetics Sequence Alignment - methods Sequence Analysis, RNA - methods Software |
| Title | MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing |
| URI | https://api.istex.fr/ark:/67375/HXZ-DLTHXHTT-Q/fulltext.pdf https://www.ncbi.nlm.nih.gov/pubmed/18006551 https://www.proquest.com/docview/198678473 https://www.proquest.com/docview/19679972 https://www.proquest.com/docview/69047115 https://academic.oup.com/bioinformatics/article-pdf/23/24/3304/49823971/bioinformatics_23_24_3304.pdf |
| UnpaywallVersion | publishedVersion |
| Volume | 23 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVAFT databaseName: Open Access Digital Library customDbUrl: eissn: 1460-2059 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0005056 issn: 1367-4811 databaseCode: KQ8 dateStart: 19960101 isFulltext: true titleUrlDefault: http://grweb.coalliance.org/oadl/oadl.html providerName: Colorado Alliance of Research Libraries – providerCode: PRVEBS databaseName: Inspec with Full Text customDbUrl: eissn: 1460-2059 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0005056 issn: 1367-4811 databaseCode: ADMLS dateStart: 19980101 isFulltext: true titleUrlDefault: https://www.ebsco.com/products/research-databases/inspec-full-text providerName: EBSCOhost – providerCode: PRVBFR databaseName: Free Medical Journals customDbUrl: eissn: 1460-2059 dateEnd: 20241103 omitProxy: true ssIdentifier: ssj0005056 issn: 1367-4811 databaseCode: DIK dateStart: 19960101 isFulltext: true titleUrlDefault: http://www.freemedicaljournals.com providerName: Flying Publisher – providerCode: PRVFQY databaseName: GFMER Free Medical Journals customDbUrl: eissn: 1460-2059 dateEnd: 20241103 omitProxy: true ssIdentifier: ssj0005056 issn: 1367-4811 databaseCode: GX1 dateStart: 19960101 isFulltext: true titleUrlDefault: http://www.gfmer.ch/Medical_journals/Free_medical.php providerName: Geneva Foundation for Medical Education and Research – providerCode: PRVAQN databaseName: PubMed Central customDbUrl: eissn: 1460-2059 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0005056 issn: 1367-4811 databaseCode: RPM dateStart: 20070101 isFulltext: true titleUrlDefault: https://www.ncbi.nlm.nih.gov/pmc/ providerName: National Library of Medicine – providerCode: PRVOVD databaseName: Journals@Ovid LWW All Open Access Journal Collection Rolling customDbUrl: eissn: 1460-2059 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0005056 issn: 1367-4811 databaseCode: OVEED dateStart: 20010101 isFulltext: true titleUrlDefault: http://ovidsp.ovid.com/ providerName: Ovid – providerCode: PRVASL databaseName: Oxford Journals Open Access Collection customDbUrl: eissn: 1460-2059 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0005056 issn: 1367-4811 databaseCode: TOX dateStart: 19850101 isFulltext: true titleUrlDefault: https://academic.oup.com/journals/ providerName: Oxford University Press – providerCode: PRVASL databaseName: Oxford Journals Open Access Collection customDbUrl: eissn: 1460-2059 dateEnd: 20220930 omitProxy: true ssIdentifier: ssj0005056 issn: 1367-4811 databaseCode: TOX dateStart: 19850101 isFulltext: true titleUrlDefault: https://academic.oup.com/journals/ providerName: Oxford University Press |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwtV1bb9MwFD7aWiFAiPslDIofEBIPaS62Y4e3CpgqxAqMTup4iezEnqZ1adWLYPwAfjfHTdKNCsR44M2Jz7Gd4yP7c3wuAM-lsFqa1PqaytBnMqK-Kmjqi1Cm2jItWe5udPcGSf-AvRvx0RaYxhdG1Vbh3calQR9P6hCiLmxxUMvTnxY2iGkQs8AdyAOWyhh31miDPItpFrPMkXSRYxvaCUfI3oL2weBj77DyyRI4xFUG5bocRY2nT0o3u9eLU-6yal_Yw9puOr41_nE3pmqOwrVVVozfwdbrcHVZTtXZVzUeX9jKdm_Bj0YIlQXLSXe50N38-0Z8yP8updtwswbDpFe1cwe2THkXrlTpMc_uQbbX-zzcf0Uao0eCZ4ajlfUCUWVBqtC3y5kh05m7bnIqRiaWlJPSzyduTyb7g96cONP-IzI_PnWZykyBvCWiY3x3Hw523w5f9_06IYSfcykWvqBmFTIvl0ILhdDDMssLoQsRKk3DXEkqreR4BhIh1zyyKcJXGkcFM0xqLD-AFo7BPALCEqVj5BZpaBgPQ13gM7dKGWUTbnIPWDPFWV5HS3dJO8ZZdWtPsw0ZVprhQXfNNq3ChfyN4cVKf9bUanbibO0Ez_qjL9mb98P-qD8cZp88eImTfdlGO7-o4TkXYo8klcyDnUYvs3rNmmOlROTCBPXg2boWFxt3g6RKM1k6kkQ4T-s_UyRpiHAnwiE8rNT9vG_p4C6PPAjW-n-5z3n8zxw7cG31Dz6K_Yg_gRbqo3mK4HGhO7A9_DDq1AvATw_Ydho |
| linkProvider | Unpaywall |
| linkToUnpaywall | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwtV1bb9MwFD4arRBMiDsjDIYfEBIPaS62Y4e3CpgqxCoYrVT2EtmJPU3r0qoXwfgB_G6Om6QbFYjxwFsSn2M7xyf25_hcAF5IYbU0qfU1laHPZER9VdDUF6FMtWVastyd6B70k96QvR_x0RaYxhdG1VbhncalQZ9M6hCiLmxxUMvTnxY2iGkQs8BtyAOWyhhX1miDPItpFrPMkXSQ4xq0E46QvQXtYf9j90vlkyWwi6sMyvV1FDWePindbF4vzrjLqn1pDWu74fjW-Mfdmqo5CtdWWTF-B1u34caynKrzr2o8vrSU7d-BH40QKguW085yoTv59434kP9dSnfhdg2GSbeq5x5smfI-XK_SY54_gOyg-3lw-Jo0Ro8E9wzHK-sFosqCVKFvlzNDpjN33ORUjEwsKSeln0_cmkwO-905cab9x2R-cuYylZkCeUtEx_jsIQz33w3e9Pw6IYSfcykWvqBmFTIvl0ILhdDDMssLoQsRKk3DXEkqreS4BxIh1zyyKcJXGkcFM0xqvH4ELeyDeQyEJUrHyC3S0DAehrrAe26VMsom3OQesGaIs7yOlu6Sdoyz6tSeZhsyrDTDg86abVqFC_kbw8uV_qyp1ezU2doJnvVGR9nbD4PeqDcYZJ88eIWDfdVK935RwwsuxB5JKpkHu41eZvWcNcdCiciFCerB83UpTjbuBEmVZrJ0JIlwntZ_pkjSEOFOhF3YqdT9om3p4C6PPAjW-n-113nyzxy7cHP1Dz6K_Yg_hRbqo3mG4HGh9-pP_ydQRXT- |
| 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=MASTR+%3A+multiple+alignment+and+structure+prediction+of+non-coding+RNAs+using+simulated+annealing&rft.jtitle=Bioinformatics+%28Oxford%2C+England%29&rft.au=LINDGREEN%2C+Stinus&rft.au=GARDNER%2C+Paul+P&rft.au=KROGH%2C+Anders&rft.date=2007-12-15&rft.pub=Oxford+University+Press&rft.issn=1367-4803&rft.volume=23&rft.issue=24&rft.spage=3304&rft.epage=3311&rft_id=info:doi/10.1093%2Fbioinformatics%2Fbtm525&rft.externalDBID=n%2Fa&rft.externalDocID=19906984 |
| 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 |