scholarly journals An Updated Functional Annotation of Protein-Coding Genes in the Cucumber Genome

2018 ◽  
Vol 9 ◽  
Author(s):  
Hongtao Song ◽  
Kui Lin ◽  
Jinglu Hu ◽  
Erli Pang
Keyword(s):  
Functional Annotation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Cucumber Genome

scholarly journals Maize GO Annotation - Methods, Evaluation, and Review (maize-GAMER)

2017 ◽  
Author(s):  
Kokulapalan Wimalanathan ◽  
Iddo Friedberg ◽  
Carson M. Andorf ◽  
Carolyn J. Lawrence-Dill
Keyword(s):  
Gold Standard ◽  
Functional Annotation ◽  
Sequence Similarity ◽  
Protein Domain ◽  
High Coverage ◽  
Protein Coding ◽  
Go Annotation ◽  
Protein Coding Genes ◽  
Standard Set ◽  
Maize Protein

1SummaryWe created a new high-coverage, robust, and reproducible functional annotation of maize protein coding genes based on Gene Ontology (GO) term assignments. Whereas the existing Phytozome and Gramene maize GO annotation sets only cover 41% and 56% of maize protein coding genes, respectively, this study provides annotations for 100% of the genes. We also compared the quality of our newly-derived annotations with the existing Gramene and Phytozome functional annotation sets by comparing all three to a manually annotated gold standard set of 1,619 genes where annotations were primarily inferred from direct assay or mutant phenotype. Evaluations based on the gold standard indicate that our new annotation set is measurably more accurate than those from Phytozome and Gramene. To derive this new high-coverage, high-confidence annotation set we used sequence-similarity and protein-domain-presence methods as well as mixed-method pipelines that developed for the Critical Assessment of Function Annotation (CAFA) challenge. Our project to improve maize annotations is called maize-GAMER (GO Annotation Method, Evaluation, and Review) and the newly-derived annotations are accessible via MaizeGDB (http://download.maizegdb.org/maize-GAMER) and CyVerse (B73 RefGen_v3 5b+ at doi: doi.org/10.7946/P2S62P and B73 RefGen_v4 Zm00001d.2 at doi: doi.org/10.7946/P2M925).

scholarly journals RNA-Seq improves annotation of protein-coding genes in the cucumber genome

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhen Li ◽  
Zhonghua Zhang ◽  
Pengcheng Yan ◽  
Sanwen Huang ◽  
Zhangjun Fei ◽  
...  
Keyword(s):  
Rna Seq ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Cucumber Genome

scholarly journals UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase

2020 ◽  
Author(s):  
Alistair MacDougall ◽  
Vladimir Volynkin ◽  
Rabie Saidi ◽  
Diego Poggioli ◽  
Hermann Zellner ◽  
...  
Keyword(s):  
Experimental Evidence ◽  
Genome Sequencing ◽  
Functional Properties ◽  
Functional Annotation ◽  
Selection Criteria ◽  
Protein Family ◽  
Automatic Annotation ◽  
Protein Coding ◽  
Protein Coding Genes

Abstract Motivation The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result of genome sequencing and the prediction of protein-coding genes. Providing functional annotation for these proteins presents a significant and continuing challenge. Results In response to this challenge, UniProt has developed a method of annotation, known as UniRule, based on expertly curated rules, which integrates related systems (RuleBase, HAMAP, PIRSR, PIRNR) developed by the members of the UniProt consortium. UniRule uses protein family signatures from InterPro, combined with taxonomic and other constraints, to select sets of reviewed proteins which have common functional properties supported by experimental evidence. This annotation is propagated to unreviewed records in UniProtKB that meet the same selection criteria, most of which do not have (and are never likely to have) experimentally verified functional annotation. Release 2020_01 of UniProtKB contains 6496 UniRule rules which provide annotation for 53 million proteins, accounting for 30% of the 178 million records in UniProtKB. UniRule provides scalable enrichment of annotation in UniProtKB. Availability and implementation UniRule rules are integrated into UniProtKB and can be viewed at https://www.uniprot.org/unirule/. UniRule rules and the code required to run the rules, are publicly available for researchers who wish to annotate their own sequences. The implementation used to run the rules is known as UniFIRE and is available at https://gitlab.ebi.ac.uk/uniprot-public/unifire.

scholarly journals Draft Genome Sequence of Curtobacterium sp. Strain ER1/6, an Endophytic Strain Isolated from Citrus sinensis with Potential To Be Used as a Biocontrol Agent

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Leandro Maza Garrido ◽  
João Marcelo Pereira Alves ◽  
Liliane Santana Oliveira ◽  
Arthur Gruber ◽  
Gabriel Padilla ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Functional Annotation ◽  
Citrus Sinensis ◽  
Biocontrol Agent ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Protein Coding Genes

Herein, we report a draft genome sequence of the endophytic Curtobacterium sp. strain ER1/6, isolated from a surface-sterilized Citrus sinensis branch, and it presented the capability to control phytopathogens. Functional annotation of the ~3.4-Mb genome revealed 3,100 protein-coding genes, with many products related to known ecological and biotechnological aspects of this bacterium.

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