UTRme: A Scoring-Based Tool to Annotate Untranslated Regions in Trypanosomatid Genomes
Most signals involved in post-transcriptional regulatory networks are located in the untranslated regions (UTRs) of the mRNAs. Therefore, to deepen our understanding of gene expression regulation, delimitation of these regions with high accuracy is needed. The trypanosomatid lineage includes a varie...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-12-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2018.00671/full |
| _version_ | 1811319016252243968 |
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| author | Santiago Radío Santiago Radío Rafael Sebastián Fort Rafael Sebastián Fort Beatriz Garat José Sotelo-Silveira José Sotelo-Silveira Pablo Smircich Pablo Smircich |
| author_facet | Santiago Radío Santiago Radío Rafael Sebastián Fort Rafael Sebastián Fort Beatriz Garat José Sotelo-Silveira José Sotelo-Silveira Pablo Smircich Pablo Smircich |
| author_sort | Santiago Radío |
| collection | DOAJ |
| description | Most signals involved in post-transcriptional regulatory networks are located in the untranslated regions (UTRs) of the mRNAs. Therefore, to deepen our understanding of gene expression regulation, delimitation of these regions with high accuracy is needed. The trypanosomatid lineage includes a variety of parasitic protozoans causing a significant worldwide burden on human health. Given their peculiar mechanisms of gene expression, these organisms depend on post-transcriptional regulation as the main level of gene expression control. In this context, the definition of the UTR regions becomes of key importance. We have developed UTR-mini-exon (UTRme), a graphical user interface (GUI) stand-alone application to identify and annotate 5′ and 3′ UTR regions in a highly accurate way. UTRme implements a multiple scoring system tailored to address the issue of false positive UTR assignment that frequently arise because of the characteristics of the intergenic regions. Even though it was developed for trypanosomatids, the tool can be used to predict 3′ sites in any eukaryote and 5′ UTRs in any organism where trans-splicing occurs (such as the model organism C. elegans). UTRme offers a way for non-bioinformaticians to precisely determine UTRs from transcriptomic data. The tool is freely available via the conda and github repositories. |
| first_indexed | 2024-04-13T12:35:02Z |
| format | Article |
| id | doaj.art-000316fd9cbb465fa644c031a386cfa8 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-13T12:35:02Z |
| publishDate | 2018-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-000316fd9cbb465fa644c031a386cfa82022-12-22T02:46:41ZengFrontiers Media S.A.Frontiers in Genetics1664-80212018-12-01910.3389/fgene.2018.00671425020UTRme: A Scoring-Based Tool to Annotate Untranslated Regions in Trypanosomatid GenomesSantiago Radío0Santiago Radío1Rafael Sebastián Fort2Rafael Sebastián Fort3Beatriz Garat4José Sotelo-Silveira5José Sotelo-Silveira6Pablo Smircich7Pablo Smircich8Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Montevideo, UruguayLaboratory of Molecular Interactions, Facultad de Ciencias. Universidad de la República, Montevideo, UruguayDepartment of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Montevideo, UruguayLaboratory of Molecular Interactions, Facultad de Ciencias. Universidad de la República, Montevideo, UruguayLaboratory of Molecular Interactions, Facultad de Ciencias. Universidad de la República, Montevideo, UruguayDepartment of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Montevideo, UruguayDepartment of Cell and Molecular Biology, Facultad de Ciencias, Universidad de la República, Montevideo, UruguayDepartment of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Montevideo, UruguayLaboratory of Molecular Interactions, Facultad de Ciencias. Universidad de la República, Montevideo, UruguayMost signals involved in post-transcriptional regulatory networks are located in the untranslated regions (UTRs) of the mRNAs. Therefore, to deepen our understanding of gene expression regulation, delimitation of these regions with high accuracy is needed. The trypanosomatid lineage includes a variety of parasitic protozoans causing a significant worldwide burden on human health. Given their peculiar mechanisms of gene expression, these organisms depend on post-transcriptional regulation as the main level of gene expression control. In this context, the definition of the UTR regions becomes of key importance. We have developed UTR-mini-exon (UTRme), a graphical user interface (GUI) stand-alone application to identify and annotate 5′ and 3′ UTR regions in a highly accurate way. UTRme implements a multiple scoring system tailored to address the issue of false positive UTR assignment that frequently arise because of the characteristics of the intergenic regions. Even though it was developed for trypanosomatids, the tool can be used to predict 3′ sites in any eukaryote and 5′ UTRs in any organism where trans-splicing occurs (such as the model organism C. elegans). UTRme offers a way for non-bioinformaticians to precisely determine UTRs from transcriptomic data. The tool is freely available via the conda and github repositories.https://www.frontiersin.org/article/10.3389/fgene.2018.00671/fullpost transcriptional regulationuntranslated regionUTR prediction softwareprediction scoreGUI |
| spellingShingle | Santiago Radío Santiago Radío Rafael Sebastián Fort Rafael Sebastián Fort Beatriz Garat José Sotelo-Silveira José Sotelo-Silveira Pablo Smircich Pablo Smircich UTRme: A Scoring-Based Tool to Annotate Untranslated Regions in Trypanosomatid Genomes Frontiers in Genetics post transcriptional regulation untranslated region UTR prediction software prediction score GUI |
| title | UTRme: A Scoring-Based Tool to Annotate Untranslated Regions in Trypanosomatid Genomes |
| title_full | UTRme: A Scoring-Based Tool to Annotate Untranslated Regions in Trypanosomatid Genomes |
| title_fullStr | UTRme: A Scoring-Based Tool to Annotate Untranslated Regions in Trypanosomatid Genomes |
| title_full_unstemmed | UTRme: A Scoring-Based Tool to Annotate Untranslated Regions in Trypanosomatid Genomes |
| title_short | UTRme: A Scoring-Based Tool to Annotate Untranslated Regions in Trypanosomatid Genomes |
| title_sort | utrme a scoring based tool to annotate untranslated regions in trypanosomatid genomes |
| topic | post transcriptional regulation untranslated region UTR prediction software prediction score GUI |
| url | https://www.frontiersin.org/article/10.3389/fgene.2018.00671/full |
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