SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem
Resumen:
Background: Spliced Leader trans-splicing is an important mechanism for the maturation of mRNAs in several lineages of eukaryotes, including several groups of parasites of great medical and economic importance. Nevertheless, its study across the tree of life is severely hindered by the problem of identifying the SL sequences that are being trans-spliced. Results: In this paper we present SLFinder, a four-step pipeline meant to identify de novo candidate SL sequences making very few assumptions regarding the SL sequence properties. The pipeline takes transcriptomic de novo assemblies and a reference genome as input and allows the user intervention on several points to account for unexpected features of the dataset. The strategy and its implementation were tested on real RNAseq data from species with and without SL Trans-Splicing. Conclusions: SLFinder is capable to identify SL candidates with good precision in a reasonable amount of time. It is especially suitable for species with unknown SL sequences, generating candidate sequences for further refining and experimental validation.
| 2020 | |
| ANII: FCE_3_2016_1_125297 | |
|
SL trans-splicing De novo assembly RNAseq data |
|
| Inglés | |
| Universidad de la República | |
| COLIBRI | |
| https://hdl.handle.net/20.500.12008/31735 | |
| Acceso abierto | |
| Licencia Creative Commons Atribución (CC - By 4.0) |
| _version_ | 1807522788989206528 |
|---|---|
| author | Calvelo, Javier |
| author2 | Juan, Hernán Koziol, Uriel Musto, Héctor Iriarte, Andrés |
| author2_role | author author author author |
| author_facet | Calvelo, Javier Juan, Hernán Koziol, Uriel Musto, Héctor Iriarte, Andrés |
| author_role | author |
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| collection | COLIBRI |
| dc.contributor.filiacion.none.fl_str_mv | Calvelo Javier, Universidad de la República (Uruguay). Facultad de Medicina. Juan Hernán, Universidad de la República (Uruguay). Facultad de Medicina. Koziol Uriel, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología. Musto Héctor, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología. Iriarte Andrés, Universidad de la República (Uruguay). Facultad de Medicina. |
| dc.creator.none.fl_str_mv | Calvelo, Javier Juan, Hernán Koziol, Uriel Musto, Héctor Iriarte, Andrés |
| dc.date.accessioned.none.fl_str_mv | 2022-05-31T12:36:50Z |
| dc.date.available.none.fl_str_mv | 2022-05-31T12:36:50Z |
| dc.date.issued.none.fl_str_mv | 2020 |
| dc.description.abstract.none.fl_txt_mv | Background: Spliced Leader trans-splicing is an important mechanism for the maturation of mRNAs in several lineages of eukaryotes, including several groups of parasites of great medical and economic importance. Nevertheless, its study across the tree of life is severely hindered by the problem of identifying the SL sequences that are being trans-spliced. Results: In this paper we present SLFinder, a four-step pipeline meant to identify de novo candidate SL sequences making very few assumptions regarding the SL sequence properties. The pipeline takes transcriptomic de novo assemblies and a reference genome as input and allows the user intervention on several points to account for unexpected features of the dataset. The strategy and its implementation were tested on real RNAseq data from species with and without SL Trans-Splicing. Conclusions: SLFinder is capable to identify SL candidates with good precision in a reasonable amount of time. It is especially suitable for species with unknown SL sequences, generating candidate sequences for further refining and experimental validation. |
| dc.description.sponsorship.none.fl_txt_mv | ANII: FCE_3_2016_1_125297 |
| dc.format.extent.es.fl_str_mv | 18 h. |
| dc.format.mimetype.es.fl_str_mv | application/pdf |
| dc.identifier.citation.es.fl_str_mv | Calvelo, J, Juan, H, Koziol, U, [y otros] "SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem". BMC Bioinformatics. [en línea] 2020, 21: 293. 18 h. DOI: 10.1186/s12859-020-03610-6 |
| dc.identifier.doi.none.fl_str_mv | 10.1186/s12859-020-03610-6 |
| dc.identifier.issn.none.fl_str_mv | 1471-2105 |
| dc.identifier.uri.none.fl_str_mv | https://hdl.handle.net/20.500.12008/31735 |
| dc.language.iso.none.fl_str_mv | en eng |
| dc.publisher.es.fl_str_mv | BMC |
| dc.relation.ispartof.es.fl_str_mv | BMC Bioinformatics, 2020, 21: 293 |
| dc.rights.license.none.fl_str_mv | Licencia Creative Commons Atribución (CC - By 4.0) |
| dc.rights.none.fl_str_mv | info:eu-repo/semantics/openAccess |
| dc.source.none.fl_str_mv | reponame:COLIBRI instname:Universidad de la República instacron:Universidad de la República |
| dc.subject.es.fl_str_mv | SL trans-splicing De novo assembly RNAseq data |
| dc.title.none.fl_str_mv | SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem |
| dc.type.es.fl_str_mv | Artículo |
| dc.type.none.fl_str_mv | info:eu-repo/semantics/article |
| dc.type.version.none.fl_str_mv | info:eu-repo/semantics/publishedVersion |
| description | Background: Spliced Leader trans-splicing is an important mechanism for the maturation of mRNAs in several lineages of eukaryotes, including several groups of parasites of great medical and economic importance. Nevertheless, its study across the tree of life is severely hindered by the problem of identifying the SL sequences that are being trans-spliced. Results: In this paper we present SLFinder, a four-step pipeline meant to identify de novo candidate SL sequences making very few assumptions regarding the SL sequence properties. The pipeline takes transcriptomic de novo assemblies and a reference genome as input and allows the user intervention on several points to account for unexpected features of the dataset. The strategy and its implementation were tested on real RNAseq data from species with and without SL Trans-Splicing. Conclusions: SLFinder is capable to identify SL candidates with good precision in a reasonable amount of time. It is especially suitable for species with unknown SL sequences, generating candidate sequences for further refining and experimental validation. |
| eu_rights_str_mv | openAccess |
| format | article |
| id | COLIBRI_a0de46f17a5a5e33381434903af3af2e |
| identifier_str_mv | Calvelo, J, Juan, H, Koziol, U, [y otros] "SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem". BMC Bioinformatics. [en línea] 2020, 21: 293. 18 h. DOI: 10.1186/s12859-020-03610-6 1471-2105 10.1186/s12859-020-03610-6 |
| instacron_str | Universidad de la República |
| institution | Universidad de la República |
| instname_str | Universidad de la República |
| language | eng |
| language_invalid_str_mv | en |
| network_acronym_str | COLIBRI |
| network_name_str | COLIBRI |
| oai_identifier_str | oai:colibri.udelar.edu.uy:20.500.12008/31735 |
| publishDate | 2020 |
| reponame_str | COLIBRI |
| repository.mail.fl_str_mv | mabel.seroubian@seciu.edu.uy |
| repository.name.fl_str_mv | COLIBRI - Universidad de la República |
| repository_id_str | 4771 |
| rights_invalid_str_mv | Licencia Creative Commons Atribución (CC - By 4.0) |
| spelling | Calvelo Javier, Universidad de la República (Uruguay). Facultad de Medicina.Juan Hernán, Universidad de la República (Uruguay). Facultad de Medicina.Koziol Uriel, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.Musto Héctor, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.Iriarte Andrés, Universidad de la República (Uruguay). Facultad de Medicina.2022-05-31T12:36:50Z2022-05-31T12:36:50Z2020Calvelo, J, Juan, H, Koziol, U, [y otros] "SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem". BMC Bioinformatics. [en línea] 2020, 21: 293. 18 h. DOI: 10.1186/s12859-020-03610-61471-2105https://hdl.handle.net/20.500.12008/3173510.1186/s12859-020-03610-6Background: Spliced Leader trans-splicing is an important mechanism for the maturation of mRNAs in several lineages of eukaryotes, including several groups of parasites of great medical and economic importance. Nevertheless, its study across the tree of life is severely hindered by the problem of identifying the SL sequences that are being trans-spliced. Results: In this paper we present SLFinder, a four-step pipeline meant to identify de novo candidate SL sequences making very few assumptions regarding the SL sequence properties. The pipeline takes transcriptomic de novo assemblies and a reference genome as input and allows the user intervention on several points to account for unexpected features of the dataset. The strategy and its implementation were tested on real RNAseq data from species with and without SL Trans-Splicing. Conclusions: SLFinder is capable to identify SL candidates with good precision in a reasonable amount of time. It is especially suitable for species with unknown SL sequences, generating candidate sequences for further refining and experimental validation.Submitted by Verdun Juan Pablo (jverdun@fcien.edu.uy) on 2022-05-30T22:46:27Z No. of bitstreams: 2 license_rdf: 19875 bytes, checksum: 9fdbed07f52437945402c4e70fa4773e (MD5) 10.1186s12859-020-03610-6.pdf: 1709416 bytes, checksum: 708545fd89784a5da0a0ca8bdc8a1cb8 (MD5)Approved for entry into archive by Faget Cecilia (lfaget@fcien.edu.uy) on 2022-05-31T12:35:12Z (GMT) No. of bitstreams: 2 license_rdf: 19875 bytes, checksum: 9fdbed07f52437945402c4e70fa4773e (MD5) 10.1186s12859-020-03610-6.pdf: 1709416 bytes, checksum: 708545fd89784a5da0a0ca8bdc8a1cb8 (MD5)Made available in DSpace by Luna Fabiana (fabiana.luna@seciu.edu.uy) on 2022-05-31T12:36:50Z (GMT). No. of bitstreams: 2 license_rdf: 19875 bytes, checksum: 9fdbed07f52437945402c4e70fa4773e (MD5) 10.1186s12859-020-03610-6.pdf: 1709416 bytes, checksum: 708545fd89784a5da0a0ca8bdc8a1cb8 (MD5) Previous issue date: 2020ANII: FCE_3_2016_1_12529718 h.application/pdfenengBMCBMC Bioinformatics, 2020, 21: 293Las obras depositadas en el Repositorio se rigen por la Ordenanza de los Derechos de la Propiedad Intelectual de la Universidad de la República.(Res. Nº 91 de C.D.C. de 8/III/1994 – D.O. 7/IV/1994) y por la Ordenanza del Repositorio Abierto de la Universidad de la República (Res. Nº 16 de C.D.C. de 07/10/2014)info:eu-repo/semantics/openAccessLicencia Creative Commons Atribución (CC - By 4.0)SL trans-splicingDe novo assemblyRNAseq dataSLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problemArtículoinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionreponame:COLIBRIinstname:Universidad de la Repúblicainstacron:Universidad de la RepúblicaCalvelo, JavierJuan, HernánKoziol, UrielMusto, HéctorIriarte, AndrésLICENSElicense.txtlicense.txttext/plain; charset=utf-84267http://localhost:8080/xmlui/bitstream/20.500.12008/31735/5/license.txt6429389a7df7277b72b7924fdc7d47a9MD55CC-LICENSElicense_urllicense_urltext/plain; charset=utf-844http://localhost:8080/xmlui/bitstream/20.500.12008/31735/2/license_urla0ebbeafb9d2ec7cbb19d7137ebc392cMD52license_textlicense_texttext/html; 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- Universidad de la Repúblicafalse |
| spellingShingle | SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem Calvelo, Javier SL trans-splicing De novo assembly RNAseq data |
| status_str | publishedVersion |
| title | SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem |
| title_full | SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem |
| title_fullStr | SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem |
| title_full_unstemmed | SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem |
| title_short | SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem |
| title_sort | SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem |
| topic | SL trans-splicing De novo assembly RNAseq data |
| url | https://hdl.handle.net/20.500.12008/31735 |
