Endhered Patterns in Matchings and RNA
An is a subset of arcs in matchings, such that the corresponding starting points are consecutive, and the same holds for the ending points. Such patterns are in one-to-one correspondence with the permutations. We focus on the occurrence frequency of such patterns in matchings and native (real-world)...
Uloženo v:
| Vydáno v: | Journal of computational biology Ročník 32; číslo 1; s. 28 |
|---|---|
| Hlavní autoři: | , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
United States
01.01.2025
|
| Témata: | |
| ISSN: | 1557-8666, 1557-8666 |
| On-line přístup: | Zjistit podrobnosti o přístupu |
| Tagy: |
Přidat tag
Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!
|
| Abstract | An
is a subset of arcs in matchings, such that the corresponding starting points are consecutive, and the same holds for the ending points. Such patterns are in one-to-one correspondence with the permutations. We focus on the occurrence frequency of such patterns in matchings and native (real-world) RNA structures with pseudoknots. We present combinatorial results related to the distribution and asymptotic behavior of the pattern 21, which corresponds to two consecutive base pairs frequently encountered in RNA, and the pattern 12, representing the archetypal minimal pseudoknot. We show that in matchings these two patterns are equidistributed, which is quite different from what we can find in native RNAs. We also examine the distribution of endhered patterns of size 3, showing how the patterns change under the transformation called
. Finally, we compute the distributions of endhered patterns of size 2 and 3 in native secondary RNA structures with pseudoknots and discuss possible outcomes of our study. |
|---|---|
| AbstractList | An
is a subset of arcs in matchings, such that the corresponding starting points are consecutive, and the same holds for the ending points. Such patterns are in one-to-one correspondence with the permutations. We focus on the occurrence frequency of such patterns in matchings and native (real-world) RNA structures with pseudoknots. We present combinatorial results related to the distribution and asymptotic behavior of the pattern 21, which corresponds to two consecutive base pairs frequently encountered in RNA, and the pattern 12, representing the archetypal minimal pseudoknot. We show that in matchings these two patterns are equidistributed, which is quite different from what we can find in native RNAs. We also examine the distribution of endhered patterns of size 3, showing how the patterns change under the transformation called
. Finally, we compute the distributions of endhered patterns of size 2 and 3 in native secondary RNA structures with pseudoknots and discuss possible outcomes of our study. An endhered (end-adhered) pattern is a subset of arcs in matchings, such that the corresponding starting points are consecutive, and the same holds for the ending points. Such patterns are in one-to-one correspondence with the permutations. We focus on the occurrence frequency of such patterns in matchings and native (real-world) RNA structures with pseudoknots. We present combinatorial results related to the distribution and asymptotic behavior of the pattern 21, which corresponds to two consecutive base pairs frequently encountered in RNA, and the pattern 12, representing the archetypal minimal pseudoknot. We show that in matchings these two patterns are equidistributed, which is quite different from what we can find in native RNAs. We also examine the distribution of endhered patterns of size 3, showing how the patterns change under the transformation called endhered twist. Finally, we compute the distributions of endhered patterns of size 2 and 3 in native secondary RNA structures with pseudoknots and discuss possible outcomes of our study.An endhered (end-adhered) pattern is a subset of arcs in matchings, such that the corresponding starting points are consecutive, and the same holds for the ending points. Such patterns are in one-to-one correspondence with the permutations. We focus on the occurrence frequency of such patterns in matchings and native (real-world) RNA structures with pseudoknots. We present combinatorial results related to the distribution and asymptotic behavior of the pattern 21, which corresponds to two consecutive base pairs frequently encountered in RNA, and the pattern 12, representing the archetypal minimal pseudoknot. We show that in matchings these two patterns are equidistributed, which is quite different from what we can find in native RNAs. We also examine the distribution of endhered patterns of size 3, showing how the patterns change under the transformation called endhered twist. Finally, we compute the distributions of endhered patterns of size 2 and 3 in native secondary RNA structures with pseudoknots and discuss possible outcomes of our study. |
| Author | Biane, Célia Nurligareev, Khaydar Hampikian, Greg Kirgizov, Sergey |
| Author_xml | – sequence: 1 givenname: Célia surname: Biane fullname: Biane, Célia organization: Laboratoire d'Informatique de Bourgogne, Université de Bourgogne, Dijon Cedex, France – sequence: 2 givenname: Greg surname: Hampikian fullname: Hampikian, Greg organization: CompGenomics, Boise, Idaho, USA – sequence: 3 givenname: Sergey orcidid: 0009-0008-0791-9526 surname: Kirgizov fullname: Kirgizov, Sergey organization: Laboratoire d'Informatique de Bourgogne, Université de Bourgogne, Dijon Cedex, France – sequence: 4 givenname: Khaydar surname: Nurligareev fullname: Nurligareev, Khaydar organization: Laboratoire d'Informatique de Bourgogne, Université de Bourgogne, Dijon Cedex, France |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/39714916$$D View this record in MEDLINE/PubMed |
| BookMark | eNpNj0tLw0AURgep2Icu3UpW4ibxTjLPZSmtFuoD0XWYzNzYSDKpmWThvzdgha6-szgc-OZk4luPhFxTSCgofW-bIkkhZQkIrs7IjHIuYyWEmJzwlMxD-AKgmQB5QaaZlpRpKmbkdu3dHjt00avpe-x8iCofPZne7iv_GSLjXfT2vLwk56WpA14dd0E-Nuv31WO8e3nYrpa72DIQfVxIx10hqRaiRA1FiQhCGcuZkZpannIAVJlmEi1o50CjZI4yJR0YqjFdkLu_7qFrvwcMfd5UwWJdG4_tEPJsdMcGE2xUb47qUDTo8kNXNab7yf-_pb9qsE_n |
| CitedBy_id | crossref_primary_10_1016_j_disc_2025_114400 |
| ContentType | Journal Article |
| DBID | CGR CUY CVF ECM EIF NPM 7X8 |
| DOI | 10.1089/cmb.2024.0658 |
| DatabaseName | Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed MEDLINE - Academic |
| DatabaseTitle | MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic |
| DatabaseTitleList | MEDLINE MEDLINE - Academic |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: 7X8 name: MEDLINE - Academic url: https://search.proquest.com/medline sourceTypes: Aggregation Database |
| DeliveryMethod | no_fulltext_linktorsrc |
| Discipline | Biology Mathematics |
| EISSN | 1557-8666 |
| ExternalDocumentID | 39714916 |
| Genre | Journal Article |
| GroupedDBID | --- 0R~ 1-M 29K 34G 39C 4.4 53G 5GY ABBKN ABEFU ACGFO ADBBV AENEX AFOSN AI. ALMA_UNASSIGNED_HOLDINGS BAWUL BNQNF CAG CGR COF CS3 CUY CVF D-I DIK DU5 EBS ECM EIF EJD F5P IAO IER IGS IHR IM4 ISR ITC MV1 NPM NQHIM O9- OK1 P2P R.V RIG RML RMSOB RNS TN5 TR2 UE5 VH1 7X8 SCNPE |
| ID | FETCH-LOGICAL-c406t-b7d5db71966fe90bfee068ac54a791c52500e83947ec09dd09e74d1487d0a19e2 |
| IEDL.DBID | 7X8 |
| ISICitedReferencesCount | 1 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=001381804600001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 1557-8666 |
| IngestDate | Thu Oct 02 12:12:06 EDT 2025 Sat Jan 11 01:32:06 EST 2025 |
| IsDoiOpenAccess | false |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 1 |
| Keywords | secondary structure pattern RNA combinatorics matching |
| Language | English |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c406t-b7d5db71966fe90bfee068ac54a791c52500e83947ec09dd09e74d1487d0a19e2 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ORCID | 0009-0008-0791-9526 |
| OpenAccessLink | https://hal.science/hal-04563757 |
| PMID | 39714916 |
| PQID | 3148500464 |
| PQPubID | 23479 |
| ParticipantIDs | proquest_miscellaneous_3148500464 pubmed_primary_39714916 |
| PublicationCentury | 2000 |
| PublicationDate | 2025-01-01 |
| PublicationDateYYYYMMDD | 2025-01-01 |
| PublicationDate_xml | – month: 01 year: 2025 text: 2025-01-01 day: 01 |
| PublicationDecade | 2020 |
| PublicationPlace | United States |
| PublicationPlace_xml | – name: United States |
| PublicationTitle | Journal of computational biology |
| PublicationTitleAlternate | J Comput Biol |
| PublicationYear | 2025 |
| SSID | ssj0013607 |
| Score | 2.4301016 |
| Snippet | An
is a subset of arcs in matchings, such that the corresponding starting points are consecutive, and the same holds for the ending points. Such patterns are... An endhered (end-adhered) pattern is a subset of arcs in matchings, such that the corresponding starting points are consecutive, and the same holds for the... |
| SourceID | proquest pubmed |
| SourceType | Aggregation Database Index Database |
| StartPage | 28 |
| SubjectTerms | Algorithms Base Pairing - genetics Computational Biology - methods Nucleic Acid Conformation RNA - chemistry RNA - genetics |
| Title | Endhered Patterns in Matchings and RNA |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/39714916 https://www.proquest.com/docview/3148500464 |
| Volume | 32 |
| WOSCitedRecordID | wos001381804600001&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1JS8NAFB7UKujBpW51I4J4i51JZjKdkxRp8WBDEYXeymzBHpxWUwX_vW8mqXoRBC85JZC8vOWb9828D6ELbXGhWMpipaWOKcMqVsJkMbOYqoxBiNFwUPiO53lnNBLDuuFW1tsqFzkxJGoz1b5H3k4Bt7NAxF3PXmKvGuXZ1VpCYxk1UoAy3qv56AeLkIXj0lAyIRMDTq9nbOKOaOtnBYvDhF75Evw7ugxVpr_13_fbRps1voy6lUPsoCXrmmitUpz8aKKNwdeY1nIXXfacefJindEwjNl0ZTRxEdwSNliWkXQmus-7e-ix33u4uY1r4YRYQ32ex4obZhSH4MoKK7AqrMVZR2pGJRdEeyYTW0BGlFuNhTFYWE4NfAA3WBJhk3204qbOHqIoITZNJCGFLgylhVDEEzckVSQzSlLeQucLc4zBMT3bIJ2dvpXjb4O00EFl0_GsmqAxBhAEKzOSHf3h6WO0nnjN3dD2OEGNAsLSnqJV_T6flK9n4Y_DNR8OPgHCH7Nd |
| linkProvider | ProQuest |
| 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=Endhered+Patterns+in+Matchings+and+RNA&rft.jtitle=Journal+of+computational+biology&rft.au=Biane%2C+C%C3%A9lia&rft.au=Hampikian%2C+Greg&rft.au=Kirgizov%2C+Sergey&rft.au=Nurligareev%2C+Khaydar&rft.date=2025-01-01&rft.eissn=1557-8666&rft.volume=32&rft.issue=1&rft.spage=28&rft_id=info:doi/10.1089%2Fcmb.2024.0658&rft_id=info%3Apmid%2F39714916&rft_id=info%3Apmid%2F39714916&rft.externalDocID=39714916 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1557-8666&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1557-8666&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1557-8666&client=summon |