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YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut
The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves exist...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
F1000Research
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4732554/ https://www.ncbi.nlm.nih.gov/pubmed/26870317 http://dx.doi.org/10.12688/f1000research.6617.2 |
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author | Chakraborty, Sandeep Britton, Monica Wegrzyn, Jill Butterfield, Timothy Martínez-García, Pedro José Reagan, Russell L. Rao, Basuthkar J. Leslie, Charles A. Aradhaya, Mallikarjuna Neale, David Woeste, Keith Dandekar, Abhaya M. |
author_facet | Chakraborty, Sandeep Britton, Monica Wegrzyn, Jill Butterfield, Timothy Martínez-García, Pedro José Reagan, Russell L. Rao, Basuthkar J. Leslie, Charles A. Aradhaya, Mallikarjuna Neale, David Woeste, Keith Dandekar, Abhaya M. |
author_sort | Chakraborty, Sandeep |
collection | PubMed |
description | The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS - Yet Another Tool Suite for analyzing RNA-seq derived transcriptome). A unique feature of YeATS is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts. We present the YeATS workflow using a representative sample of the transcriptome from the tissue at the heartwood/sapwood transition zone in black walnut. A novel feature of the transcriptome that emerged from our analysis was the identification of a highly abundant transcript that had no known homologous genes (GenBank accession: KT023102). The amino acid composition of the longest open reading frame of this gene classifies this as a putative extensin. Also, we corroborated the transcriptional abundance of proline-rich proteins, dehydrins, senescence-associated proteins, and the DNAJ family of chaperone proteins. Thus, YeATS presents a workflow for analyzing RNA-seq data with several innovative features that differentiate it from existing software. |
format | Online Article Text |
id | pubmed-4732554 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | F1000Research |
record_format | MEDLINE/PubMed |
spelling | pubmed-47325542016-02-10 YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut Chakraborty, Sandeep Britton, Monica Wegrzyn, Jill Butterfield, Timothy Martínez-García, Pedro José Reagan, Russell L. Rao, Basuthkar J. Leslie, Charles A. Aradhaya, Mallikarjuna Neale, David Woeste, Keith Dandekar, Abhaya M. F1000Res Research Article The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS - Yet Another Tool Suite for analyzing RNA-seq derived transcriptome). A unique feature of YeATS is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts. We present the YeATS workflow using a representative sample of the transcriptome from the tissue at the heartwood/sapwood transition zone in black walnut. A novel feature of the transcriptome that emerged from our analysis was the identification of a highly abundant transcript that had no known homologous genes (GenBank accession: KT023102). The amino acid composition of the longest open reading frame of this gene classifies this as a putative extensin. Also, we corroborated the transcriptional abundance of proline-rich proteins, dehydrins, senescence-associated proteins, and the DNAJ family of chaperone proteins. Thus, YeATS presents a workflow for analyzing RNA-seq data with several innovative features that differentiate it from existing software. F1000Research 2015-11-06 /pmc/articles/PMC4732554/ /pubmed/26870317 http://dx.doi.org/10.12688/f1000research.6617.2 Text en Copyright: © 2015 Chakraborty S et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Chakraborty, Sandeep Britton, Monica Wegrzyn, Jill Butterfield, Timothy Martínez-García, Pedro José Reagan, Russell L. Rao, Basuthkar J. Leslie, Charles A. Aradhaya, Mallikarjuna Neale, David Woeste, Keith Dandekar, Abhaya M. YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut |
title | YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut |
title_full | YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut |
title_fullStr | YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut |
title_full_unstemmed | YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut |
title_short | YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut |
title_sort | yeats - a tool suite for analyzing rna-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4732554/ https://www.ncbi.nlm.nih.gov/pubmed/26870317 http://dx.doi.org/10.12688/f1000research.6617.2 |
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