AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers

Autores
Ruiz Ciancio, Dario Ezequiel; Veeramani, Suresh; Embree, Eric; Ortman, Chris; Thiel, Kristina W.; Thiel, William H.
Año de publicación
2023
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Aptamers are short single-stranded DNA or RNA molecules with high affinity and specificity for targets and are generated using the iterative Systematic Evolution of Ligands by EXponential enrichment (SELEX) process. Next-generation sequencing (NGS) revolutionized aptamer selections by allowing a more comprehensive analysis of SELEX-enriched aptamers as compared to Sanger sequencing. The current challenge with aptamer NGS datasets is identifying a diverse cohort of candidate aptamers with the highest likelihood of successful experimental validation. Herein we present AptamerRunner, an aptamer clustering algorithm that generates visual networks of aptamers that are related by sequence and/or structure. These networks can then be overlayed with ranking data, such as fold enrichment or data from scoring algorithms. The ability to visually integrate data using AptamerRunner represents a significant advancement over existing clustering tools by providing a natural context to depict groups of aptamers from which ranked or scored candidates can be chosen for experimental validation. The inherent flexibility, user-friendly design, and prospects for future enhancements with AptamerRunner has broad-reaching implications for aptamer researchers across a wide range of disciplines.
Fil: Ruiz Ciancio, Dario Ezequiel. Universidad Catolica de Cuyo. Facultad de Ciencias Medicas. Instituto de Investigacion En Ciencias Biomedicas.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina
Fil: Veeramani, Suresh. University of Iowa; Estados Unidos
Fil: Embree, Eric. University of Iowa; Estados Unidos
Fil: Ortman, Chris. University of Iowa; Estados Unidos
Fil: Thiel, Kristina W.. University of Iowa; Estados Unidos
Fil: Thiel, William H.. University of Iowa; Estados Unidos
Materia
APTAMERS
CLUSTERING ALGORTIHMS
STRUCTURE
CYTOSCAPE
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/227521
Acceder
id CONICETDig_61fff12291a5b1fa5384c2d014e9a0bc
oai_identifier_str oai:ri.conicet.gov.ar:11336/227521
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamersRuiz Ciancio, Dario EzequielVeeramani, SureshEmbree, EricOrtman, ChrisThiel, Kristina W.Thiel, William H.APTAMERSCLUSTERING ALGORTIHMSSTRUCTURECYTOSCAPEhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Aptamers are short single-stranded DNA or RNA molecules with high affinity and specificity for targets and are generated using the iterative Systematic Evolution of Ligands by EXponential enrichment (SELEX) process. Next-generation sequencing (NGS) revolutionized aptamer selections by allowing a more comprehensive analysis of SELEX-enriched aptamers as compared to Sanger sequencing. The current challenge with aptamer NGS datasets is identifying a diverse cohort of candidate aptamers with the highest likelihood of successful experimental validation. Herein we present AptamerRunner, an aptamer clustering algorithm that generates visual networks of aptamers that are related by sequence and/or structure. These networks can then be overlayed with ranking data, such as fold enrichment or data from scoring algorithms. The ability to visually integrate data using AptamerRunner represents a significant advancement over existing clustering tools by providing a natural context to depict groups of aptamers from which ranked or scored candidates can be chosen for experimental validation. The inherent flexibility, user-friendly design, and prospects for future enhancements with AptamerRunner has broad-reaching implications for aptamer researchers across a wide range of disciplines.Fil: Ruiz Ciancio, Dario Ezequiel. Universidad Catolica de Cuyo. Facultad de Ciencias Medicas. Instituto de Investigacion En Ciencias Biomedicas.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; ArgentinaFil: Veeramani, Suresh. University of Iowa; Estados UnidosFil: Embree, Eric. University of Iowa; Estados UnidosFil: Ortman, Chris. University of Iowa; Estados UnidosFil: Thiel, Kristina W.. University of Iowa; Estados UnidosFil: Thiel, William H.. University of Iowa; Estados UnidosCold Spring Harbor Laboratory Press2023-11info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/227521Ruiz Ciancio, Dario Ezequiel; Veeramani, Suresh; Embree, Eric; Ortman, Chris; Thiel, Kristina W.; et al.; AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers; Cold Spring Harbor Laboratory Press; bioRxiv; 11; 11-2023; 1-452692-82052692-8205CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://pubmed.ncbi.nlm.nih.gov/38014343/info:eu-repo/semantics/altIdentifier/doi/10.1101/2023.11.13.566453info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T10:06:14Zoai:ri.conicet.gov.ar:11336/227521instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 10:06:14.684CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers
title AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers
spellingShingle AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers
Ruiz Ciancio, Dario Ezequiel
APTAMERS
CLUSTERING ALGORTIHMS
STRUCTURE
CYTOSCAPE
title_short AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers
title_full AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers
title_fullStr AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers
title_full_unstemmed AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers
title_sort AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers
dc.creator.none.fl_str_mv Ruiz Ciancio, Dario Ezequiel
Veeramani, Suresh
Embree, Eric
Ortman, Chris
Thiel, Kristina W.
Thiel, William H.
author Ruiz Ciancio, Dario Ezequiel
author_facet Ruiz Ciancio, Dario Ezequiel
Veeramani, Suresh
Embree, Eric
Ortman, Chris
Thiel, Kristina W.
Thiel, William H.
author_role author
author2 Veeramani, Suresh
Embree, Eric
Ortman, Chris
Thiel, Kristina W.
Thiel, William H.
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv APTAMERS
CLUSTERING ALGORTIHMS
STRUCTURE
CYTOSCAPE
topic APTAMERS
CLUSTERING ALGORTIHMS
STRUCTURE
CYTOSCAPE
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Aptamers are short single-stranded DNA or RNA molecules with high affinity and specificity for targets and are generated using the iterative Systematic Evolution of Ligands by EXponential enrichment (SELEX) process. Next-generation sequencing (NGS) revolutionized aptamer selections by allowing a more comprehensive analysis of SELEX-enriched aptamers as compared to Sanger sequencing. The current challenge with aptamer NGS datasets is identifying a diverse cohort of candidate aptamers with the highest likelihood of successful experimental validation. Herein we present AptamerRunner, an aptamer clustering algorithm that generates visual networks of aptamers that are related by sequence and/or structure. These networks can then be overlayed with ranking data, such as fold enrichment or data from scoring algorithms. The ability to visually integrate data using AptamerRunner represents a significant advancement over existing clustering tools by providing a natural context to depict groups of aptamers from which ranked or scored candidates can be chosen for experimental validation. The inherent flexibility, user-friendly design, and prospects for future enhancements with AptamerRunner has broad-reaching implications for aptamer researchers across a wide range of disciplines.
Fil: Ruiz Ciancio, Dario Ezequiel. Universidad Catolica de Cuyo. Facultad de Ciencias Medicas. Instituto de Investigacion En Ciencias Biomedicas.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina
Fil: Veeramani, Suresh. University of Iowa; Estados Unidos
Fil: Embree, Eric. University of Iowa; Estados Unidos
Fil: Ortman, Chris. University of Iowa; Estados Unidos
Fil: Thiel, Kristina W.. University of Iowa; Estados Unidos
Fil: Thiel, William H.. University of Iowa; Estados Unidos
description Aptamers are short single-stranded DNA or RNA molecules with high affinity and specificity for targets and are generated using the iterative Systematic Evolution of Ligands by EXponential enrichment (SELEX) process. Next-generation sequencing (NGS) revolutionized aptamer selections by allowing a more comprehensive analysis of SELEX-enriched aptamers as compared to Sanger sequencing. The current challenge with aptamer NGS datasets is identifying a diverse cohort of candidate aptamers with the highest likelihood of successful experimental validation. Herein we present AptamerRunner, an aptamer clustering algorithm that generates visual networks of aptamers that are related by sequence and/or structure. These networks can then be overlayed with ranking data, such as fold enrichment or data from scoring algorithms. The ability to visually integrate data using AptamerRunner represents a significant advancement over existing clustering tools by providing a natural context to depict groups of aptamers from which ranked or scored candidates can be chosen for experimental validation. The inherent flexibility, user-friendly design, and prospects for future enhancements with AptamerRunner has broad-reaching implications for aptamer researchers across a wide range of disciplines.
publishDate 2023
dc.date.none.fl_str_mv 2023-11
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/227521
Ruiz Ciancio, Dario Ezequiel; Veeramani, Suresh; Embree, Eric; Ortman, Chris; Thiel, Kristina W.; et al.; AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers; Cold Spring Harbor Laboratory Press; bioRxiv; 11; 11-2023; 1-45
2692-8205
2692-8205
CONICET Digital
CONICET
url http://hdl.handle.net/11336/227521
identifier_str_mv Ruiz Ciancio, Dario Ezequiel; Veeramani, Suresh; Embree, Eric; Ortman, Chris; Thiel, Kristina W.; et al.; AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers; Cold Spring Harbor Laboratory Press; bioRxiv; 11; 11-2023; 1-45
2692-8205
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://pubmed.ncbi.nlm.nih.gov/38014343/
info:eu-repo/semantics/altIdentifier/doi/10.1101/2023.11.13.566453
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Cold Spring Harbor Laboratory Press
publisher.none.fl_str_mv Cold Spring Harbor Laboratory Press
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1842269948378873856
score 13.13397

Publicaciones similares