Malus x domestica Golden Delicious Genome NCBI annotation
Overview
Publication: Daccord N, Celton JM, Linsmith G, Becker C, Choisne N, Schijlen E, van de Geest H, Bianco L, Micheletti D, Velasco R, Di Pierro EA, Gouzy J, Rees DJG, Guérif P, Muranty H, Durel CE, Laurens F, Lespinasse Y, Gaillard S, Aubourg S, Quesneville H, Weigel D, van de Weg E, Troggio M, Bucher E. (2017) High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nature genetics. 49, 1099–1106 Original Annotation Data is available at Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation Assembly statistics (Re-annotation done by NCBI)
BUSCO analysis (4.0.2)
Homology
Homology of the Malus x domestica Golden Delicious genome v1.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-6 for the Arabidoposis proteins (Araport11, 2022-09), UniProtKB/SwissProt (Release 2023-07), and UniProtKB/TrEMBL (Release 2023-07) databases. The best hit reports are available for download in Excel format. Protein Homologs
Assembly
The Malus x domestica Golden Delicious NCBI genome v1.0 assembly files are available in GFF3 and FASTA format. Downloads
Gene Predictions
The Malus x domestica NCBI genome v1.0 gene prediction files are available in GFF3 and FASTA format. Downloads
Functional Analysis
Functional annotation for the Malus x domestica Golden Delicious genome v1.0 are available for download below. The Malus x domestica genome v1.0 proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS). Downloads
Transcript Alignments
Transcript alignments were performed by the GDR Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the Malus x domestica Golden Delicious NCBI annotation. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.
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