Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing
Annotation of the rice (Oryza sativa) genome has evolved significantly since release of its draft sequence, but it is far from complete. Several published transcript assembly programmes were tested on RNA-sequencing (RNA-seq) data to determine their effectiveness in identifying novel genes to improv...
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| Format: | Online |
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Oxford University Press
2015
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4596398/ |
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pubmed-45963982015-10-09 Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing Watanabe, Kenneth A. Homayouni, Arielle Tufano, Tara Lopez, Jennifer Ringler, Patricia Rushton, Paul Shen, Qingxi J. Full Papers Annotation of the rice (Oryza sativa) genome has evolved significantly since release of its draft sequence, but it is far from complete. Several published transcript assembly programmes were tested on RNA-sequencing (RNA-seq) data to determine their effectiveness in identifying novel genes to improve the rice genome annotation. Cufflinks, a popular assembly software, did not identify all transcripts suggested by the RNA-seq data. Other assembly software was CPU intensive, lacked documentation, or lacked software updates. To overcome these shortcomings, a heuristic ab initio transcript assembly algorithm, Tiling Assembly, was developed to identify genes based on short read and junction alignment. Tiling Assembly was compared with Cufflinks to evaluate its gene-finding capabilities. Additionally, a pipeline was developed to eliminate false-positive gene identification due to noise or repetitive regions in the genome. By combining Tiling Assembly and Cufflinks, 767 unannotated genes were identified in the rice genome, demonstrating that combining both programmes proved highly efficient for novel gene identification. We also demonstrated that Tiling Assembly can accurately determine transcription start sites by comparing the Tiling Assembly genes with their corresponding full-length cDNA. We applied our pipeline to additional organisms and identified numerous unannotated genes, demonstrating that Tiling Assembly is an organism-independent tool for genome annotation. Oxford University Press 2015-10 2015-09-03 /pmc/articles/PMC4596398/ /pubmed/26341416 http://dx.doi.org/10.1093/dnares/dsv015 Text en © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Watanabe, Kenneth A. Homayouni, Arielle Tufano, Tara Lopez, Jennifer Ringler, Patricia Rushton, Paul Shen, Qingxi J. |
| spellingShingle |
Watanabe, Kenneth A. Homayouni, Arielle Tufano, Tara Lopez, Jennifer Ringler, Patricia Rushton, Paul Shen, Qingxi J. Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing |
| author_facet |
Watanabe, Kenneth A. Homayouni, Arielle Tufano, Tara Lopez, Jennifer Ringler, Patricia Rushton, Paul Shen, Qingxi J. |
| author_sort |
Watanabe, Kenneth A. |
| title |
Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing |
| title_short |
Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing |
| title_full |
Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing |
| title_fullStr |
Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing |
| title_full_unstemmed |
Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing |
| title_sort |
tiling assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by rna-sequencing |
| description |
Annotation of the rice (Oryza sativa) genome has evolved significantly since release of its draft sequence, but it is far from complete. Several published transcript assembly programmes were tested on RNA-sequencing (RNA-seq) data to determine their effectiveness in identifying novel genes to improve the rice genome annotation. Cufflinks, a popular assembly software, did not identify all transcripts suggested by the RNA-seq data. Other assembly software was CPU intensive, lacked documentation, or lacked software updates. To overcome these shortcomings, a heuristic ab initio transcript assembly algorithm, Tiling Assembly, was developed to identify genes based on short read and junction alignment. Tiling Assembly was compared with Cufflinks to evaluate its gene-finding capabilities. Additionally, a pipeline was developed to eliminate false-positive gene identification due to noise or repetitive regions in the genome. By combining Tiling Assembly and Cufflinks, 767 unannotated genes were identified in the rice genome, demonstrating that combining both programmes proved highly efficient for novel gene identification. We also demonstrated that Tiling Assembly can accurately determine transcription start sites by comparing the Tiling Assembly genes with their corresponding full-length cDNA. We applied our pipeline to additional organisms and identified numerous unannotated genes, demonstrating that Tiling Assembly is an organism-independent tool for genome annotation. |
| publisher |
Oxford University Press |
| publishDate |
2015 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4596398/ |
| _version_ |
1613484575729647616 |