CPGAVAS2, an integrated plastome sequence annotator and analyzer
| العنوان: | CPGAVAS2, an integrated plastome sequence annotator and analyzer |
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| المؤلفون: | Xi Wu, Liqiang Wang, Chang Liu, Mei Jiang, Linfang Huang, Linchun Shi, Haimei Chen |
| المصدر: | Nucleic Acids Research |
| بيانات النشر: | Oxford University Press (OUP), 2019. |
| سنة النشر: | 2019 |
| مصطلحات موضوعية: | Internet, Web server, Molecular Sequence Annotation, Sequence alignment, Exons, Computational biology, Biology, computer.software_genre, Genome, Annotation, GenBank, Web Server Issue, Genetics, Humans, RNA Editing, Databases, Nucleic Acid, Sequence Alignment, computer, Genome, Plant, Software, Sequence (medicine), Reference genome |
| الوصف: | We previously developed a web server CPGAVAS for annotation, visualization and GenBank submission of plastome sequences. Here, we upgrade the server into CPGAVAS2 to address the following challenges: (i) inaccurate annotation in the reference sequence likely causing the propagation of errors; (ii) difficulty in the annotation of small exons of genes petB, petD and rps16 and trans-splicing gene rps12; (iii) lack of annotation for other genome features and their visualization, such as repeat elements; and (iv) lack of modules for diversity analysis of plastomes. In particular, CPGAVAS2 provides two reference datasets for plastome annotation. The first dataset contains 43 plastomes whose annotation have been validated or corrected by RNA-seq data. The second one contains 2544 plastomes curated with sequence alignment. Two new algorithms are also implemented to correctly annotate small exons and trans-splicing genes. Tandem and dispersed repeats are identified, whose results are displayed on a circular map together with the annotated genes. DNA-seq and RNA-seq data can be uploaded for identification of single-nucleotide polymorphism sites and RNA-editing sites. The results of two case studies show that CPGAVAS2 annotates better than several other servers. CPGAVAS2 will likely become an indispensible tool for plastome research and can be accessed from http://www.herbalgenomics.org/cpgavas2Test. |
| تدمد: | 1362-4962 0305-1048 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::478e1c267df4512e383a1b7c1e76a512Test https://doi.org/10.1093/nar/gkz345Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....478e1c267df4512e383a1b7c1e76a512 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 13624962 03051048 |
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