Computational Environment for Genomic Sequencing and Annotation: a workflow for application in projects by life researchers
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| Format: | Artículo científico |
| Language: | en |
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Universidad Nacional de Misiones
2022
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| _version_ | 1876479630989328384 |
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| author | Matheus Pedron, Cassol |
| author_facet | Matheus Pedron, Cassol |
| contents | Computational Environment for Genomic Sequencing and Annotation: a workflow for application in projects by life researchers Matheus Pedron, Cassol Alexandre Rafael, Lenz Rudinei, Zacaria Scheila, de Avila e Silva Geología genome workflow assemble Bioinformatic computational tools The current paper seeks to approach, using a workflow, basics subjects of the bioinformatic field and also useful informations to consider during the development of in silico researches. Installation and general usage of multiple softwares related to different sections of the genome annotation process were also presented. At last, an model organism, Staphylococcus aureus, was sequenced in two different softwares, SPAdes and IDBA-UD, seeking further comparison and evaluation of the process as a whole. The quality evaluation of the assemble was established by tests on QUAST, BUSCO and Augustus, supported by BLASTP.Results: QUAST evaluation returned genome coverage values above 98% in both test cases, pointing towards a trustworthy assemble for this organism. Via SPAdes were needed less computational resources, but, using IDBA-UD the sequences found were more contiguous. Results deriving from BUSCO showed only one expected gene difference. Some proteins and genes predicted by Augustus led to hits, sequences already studied in that organism, using the BLASTP program. 2022 artículo científico 0329-8922 https://www.redalyc.org/articulo.oa?id=382679632008 https://www.redalyc.org/journal/3826/382679632008/ https://www.redalyc.org/journal/3826/382679632008/html/ https://www.redalyc.org/journal/3826/382679632008/382679632008.epub https://www.redalyc.org/journal/3826/382679632008/movil 10.36995/j.recyt.2022.38.008 en http://www.redalyc.org/revista.oa?id=3826 Revista de Ciencia y Tecnología application/pdf Universidad Nacional de Misiones Revista de Ciencia y Tecnología (Argentina) Num.1 Vol.38 |
| format | Artículo científico |
| id | redalyc_382679632008 |
| institution | Redalyc |
| language | en |
| publishDate | 2022 |
| publisher | Universidad Nacional de Misiones |
| spellingShingle | Computational Environment for Genomic Sequencing and Annotation: a workflow for application in projects by life researchers Matheus Pedron, Cassol Geología genome workflow assemble Bioinformatic computational tools Computational Environment for Genomic Sequencing and Annotation: a workflow for application in projects by life researchers Matheus Pedron, Cassol Alexandre Rafael, Lenz Rudinei, Zacaria Scheila, de Avila e Silva Geología genome workflow assemble Bioinformatic computational tools The current paper seeks to approach, using a workflow, basics subjects of the bioinformatic field and also useful informations to consider during the development of in silico researches. Installation and general usage of multiple softwares related to different sections of the genome annotation process were also presented. At last, an model organism, Staphylococcus aureus, was sequenced in two different softwares, SPAdes and IDBA-UD, seeking further comparison and evaluation of the process as a whole. The quality evaluation of the assemble was established by tests on QUAST, BUSCO and Augustus, supported by BLASTP.Results: QUAST evaluation returned genome coverage values above 98% in both test cases, pointing towards a trustworthy assemble for this organism. Via SPAdes were needed less computational resources, but, using IDBA-UD the sequences found were more contiguous. Results deriving from BUSCO showed only one expected gene difference. Some proteins and genes predicted by Augustus led to hits, sequences already studied in that organism, using the BLASTP program. 2022 artículo científico 0329-8922 https://www.redalyc.org/articulo.oa?id=382679632008 https://www.redalyc.org/journal/3826/382679632008/ https://www.redalyc.org/journal/3826/382679632008/html/ https://www.redalyc.org/journal/3826/382679632008/382679632008.epub https://www.redalyc.org/journal/3826/382679632008/movil 10.36995/j.recyt.2022.38.008 en http://www.redalyc.org/revista.oa?id=3826 Revista de Ciencia y Tecnología application/pdf Universidad Nacional de Misiones Revista de Ciencia y Tecnología (Argentina) Num.1 Vol.38 |
| title | Computational Environment for Genomic Sequencing and Annotation: a workflow for application in projects by life researchers |
| topic | Geología genome workflow assemble Bioinformatic computational tools |
| url | https://www.redalyc.org/articulo.oa?id=382679632008 https://www.redalyc.org/journal/3826/382679632008/ https://www.redalyc.org/journal/3826/382679632008/html/ https://www.redalyc.org/journal/3826/382679632008/382679632008.epub https://www.redalyc.org/journal/3826/382679632008/movil |