3 results on '"Rajdeep S Khangura"'
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2. Double triage to identify poorly annotated genes in maize: The missing link in community curation.
- Author
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Marcela K Tello-Ruiz, Cristina F Marco, Fei-Man Hsu, Rajdeep S Khangura, Pengfei Qiao, Sirjan Sapkota, Michelle C Stitzer, Rachael Wasikowski, Hao Wu, Junpeng Zhan, Kapeel Chougule, Lindsay C Barone, Cornel Ghiban, Demitri Muna, Andrew C Olson, Liya Wang, Doreen Ware, and David A Micklos
- Subjects
Medicine ,Science - Abstract
The sophistication of gene prediction algorithms and the abundance of RNA-based evidence for the maize genome may suggest that manual curation of gene models is no longer necessary. However, quality metrics generated by the MAKER-P gene annotation pipeline identified 17,225 of 130,330 (13%) protein-coding transcripts in the B73 Reference Genome V4 gene set with models of low concordance to available biological evidence. Working with eight graduate students, we used the Apollo annotation editor to curate 86 transcript models flagged by quality metrics and a complimentary method using the Gramene gene tree visualizer. All of the triaged models had significant errors-including missing or extra exons, non-canonical splice sites, and incorrect UTRs. A correct transcript model existed for about 60% of genes (or transcripts) flagged by quality metrics; we attribute this to the convention of elevating the transcript with the longest coding sequence (CDS) to the canonical, or first, position. The remaining 40% of flagged genes resulted in novel annotations and represent a manual curation space of about 10% of the maize genome (~4,000 protein-coding genes). MAKER-P metrics have a specificity of 100%, and a sensitivity of 85%; the gene tree visualizer has a specificity of 100%. Together with the Apollo graphical editor, our double triage provides an infrastructure to support the community curation of eukaryotic genomes by scientists, students, and potentially even citizen scientists.
- Published
- 2019
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3. Double triage to identify poorly annotated genes in maize: The missing link in community curation
- Author
-
Cornel Ghiban, Cristina F. Marco, Junpeng Zhan, Marcela K. Tello-Ruiz, Demitri Muna, Fei-Man Hsu, Michelle C. Stitzer, Rachael Wasikowski, Pengfei Qiao, Lindsay Barone, Doreen Ware, Sirjan Sapkota, Liya Wang, David A. Micklos, Rajdeep S. Khangura, Andrew Olson, Kapeel Chougule, and Hao Wu
- Subjects
0106 biological sciences ,Critical Care and Emergency Medicine ,Plant Science ,Plant Genetics ,01 natural sciences ,Genome ,Database and Informatics Methods ,Exon ,Databases, Genetic ,Invertebrate Genomics ,Plant Genomics ,Medicine and Health Sciences ,Coding region ,Data Curation ,Plant Proteins ,Data Management ,2. Zero hunger ,0303 health sciences ,Multidisciplinary ,Eukaryota ,Phylogenetic Analysis ,Genome project ,Genomics ,Plants ,Functional Genomics ,Phylogenetics ,Molecular Sequence Annotation ,Experimental Organism Systems ,Engineering and Technology ,Medicine ,Sequence Analysis ,Algorithms ,Research Article ,Biotechnology ,Computer and Information Sciences ,Bioinformatics ,Gene prediction ,Science ,Bioengineering ,Computational biology ,Biology ,Research and Analysis Methods ,Zea mays ,03 medical and health sciences ,Annotation ,Model Organisms ,Plant and Algal Models ,Genetics ,Humans ,Evolutionary Systematics ,Education, Graduate ,Grasses ,Students ,Gene ,Taxonomy ,030304 developmental biology ,Evolutionary Biology ,Models, Genetic ,Organisms ,Biology and Life Sciences ,Computational Biology ,Gene Annotation ,Genome Analysis ,Genome Annotation ,Maize ,Animal Genomics ,Animal Studies ,Plant Biotechnology ,Triage ,Sequence Alignment ,010606 plant biology & botany ,Reference genome - Abstract
The sophistication of gene prediction algorithms and the abundance of RNA-based evidence for the maize genome may suggest that manual curation of gene models is no longer necessary. However, quality metrics generated by the MAKER-P gene annotation pipeline identified 17,225 of 130,330 (13%) protein-coding transcripts in the B73 Reference Genome V4 gene set with models of low concordance to available biological evidence. Working with eight graduate students, we used the Apollo annotation editor to curate 86 transcript models flagged by quality metrics and a complimentary method using the Gramene gene tree visualizer. All of the triaged models had significant errors โ including missing or extra exons, non-canonical splice sites, and incorrect UTRs. A correct transcript model existed for about 60% of genes (or transcripts) flagged by quality metrics; we attribute this to the convention of elevating the transcript with the longest coding sequence (CDS) to the canonical, or first, position. The remaining 40% of flagged genes resulted in novel annotations and represent a manual curation space of about 10% of the maize genome (~4,000 protein-coding genes). MAKER-P metrics have a specificity of 100%, and a sensitivity of 85%; the gene tree visualizer has a specificity of 100%. Together with the Apollo graphical editor, our double triage provides an infrastructure to support the community curation of eukaryotic genomes by scientists, students, and potentially even citizen scientists.
- Published
- 2019
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