Name | Description | Type |
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Whole Genome Assembly and Annotation of Oryza glaberrima |
Assembly The genome sequence was generated with PacBio technology and assembled by the Arizona Genomics Institute (AGI) using strain IRGC:96717, deposited in Genbank with project accession number ADWL02000000. Annotation Protein-coding genes were annotated with MAKER-P software in CSHL. Source : Gramene |
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Whole Genome Assembly and Annotation of Oryza barthii |
Assembly The genome sequence was generated and assembled by the Arizona Genomics Institute (AGI) using project accession ABRL03000000. The sequence data were generated by PacBio technology. Annotation Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline at CSHL. Source : Gramene |
Annotation of a genome. |
Whole Genome Assembly and Annotation of Asian rice (Zhou et al, 2020) |
Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline (Campbell et al, 2014) using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP (Korf, 2004), Augustus (Stanke et al, 2008), and FGENESH (Soovyev et al, 2006) gene predictors. The combined gene models were improved for structure including UTR... read more |
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Genome sequencing and assembly of 12 rice varieties |
Genome assemblies from 12 rice varieties (https://doi.org/10.1038/s41597-020-0438-2) |
Sequence assembly capable on a very large scale such as assembly of whole genomes. [http://edamontology.org] |
Whole Genome Assembly and Annotation for Nerica L19 | ||
Whole Genome Assembly and Annotation for Nerica4 | ||
Whole Genome Assembly and Annotation of Oryza rufipogon |
Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline. Non coding RNA genes were predicted with Infernal and tRNA genes with tRNAscan. RepeatMasker was used to annotate repeats and transposable elements with Oryza-specific de novo repeat libraries. These analyses were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing. |
Annotation of a genome. |
Whole Genome Assembly and Annotation of Oryza punctata |
Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline. Non coding RNA genes were predicted with Infernal and tRNA genes with tRNAscan. RepeatMasker was used to annotate repeats and transposable elements with Oryza-specific de novo repeat libraries. These analyses were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing. |
Annotation of a genome. |
Whole Genome Assembly and Annotation of Oryza meridionalis |
Protein-coding gene annotation was performed with evidence-based MAKER-P genome annotation pipeline. Non coding RNA genes were predicted with Infernal and tRNA genes with tRNAscan. RepeatMasker was used to annotate repeats and transposable elements with Oryza-specific de novo repeat libraries. These analyses were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing. |
Annotation of a genome. |
Whole Genome Assembly and Annotation of Oryza longistaminata |
Protein-coding genes, annotation of repeats and transposable elements were conducted at Arizona Genomics Institute (AGI) led by Dr. Rod Wing. MAKER-P was used as evidence-based genome annotation pipeline. RepeatMasker was used to annotate repeats and transposable elements using species-specific de novo repeat libraries. Non coding RNA genes were predicted by AGI with Infernal, tRNA genes with tRNAScan. |
Annotation of a genome. |