Gene Annotation Easy Viewer (GAEV): Integrating KEGG’s Gene Function Annotations and Associated Molecular Pathways [version 3; peer review: 1 approved, 2 approved with reservations] [PDF]
F1000Research, 2019 We developed a Gene Annotation Easy Viewer (GAEV) that integrates the gene annotation data from the KEGG (Kyoto Encyclopedia of Genes and Genomes) Automatic Annotation Server.
Trung Huynh, Sen Xu
doaj +6 more sources
The Ensembl gene annotation system [PDF]
Database, 2016 The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets.
Bronwen L. Aken +24 more
semanticscholar +4 more sources
COGNATE: comparative gene annotation characterizer
BMC Genomics, 2017 Background The comparison of gene and genome structures across species has the potential to reveal major trends of genome evolution. However, such a comparative approach is currently hampered by a lack of standardization (e.g., Elliott TA, Gregory TR ...
Jeanne Wilbrandt +2 more
doaj +4 more sources
Gene annotation bias impedes biomedical research [PDF]
Scientific Reports, 2017 We found tremendous inequality across gene and protein annotation resources. We observed that this bias leads biomedical researchers to focus on richly annotated genes instead of those with the strongest molecular data.
W. Haynes, Aurelie Tomczak, P. Khatri
semanticscholar +3 more sources
Hayai-Annotation: A functional gene prediction tool that integrates orthologs and gene ontology for network analysis in plant species [PDF]
Computational and Structural Biotechnology JournalHayai-Annotation, an annotation tool powered by the R-shinydashboard browser interface, implements a workflow that integrates sequence alignment using DIAMOND against UniProtKB Plants and ortholog inference using OrthoLoger. We here propose a pipeline to
Andrea Ghelfi, Sachiko Isobe
doaj +2 more sources
Consistent annotation of gene expression arrays [PDF]
BMC Genomics, 2010 Background Gene expression arrays are valuable and widely used tools for biomedical research. Today's commercial arrays attempt to measure the expression level of all of the genes in the genome.
Proctor Glenn +3 more
doaj +4 more sources
Combining gene prediction methods to improve metagenomic gene annotation [PDF]
BMC Bioinformatics, 2011 Background Traditional gene annotation methods rely on characteristics that may not be available in short reads generated from next generation technology, resulting in suboptimal performance for metagenomic (environmental) samples.
Rosen Gail L, Yok Non G
doaj +3 more sources
Gene characterization index: assessing the depth of gene annotation.
PLoS ONE, 2008 BackgroundWe introduce the Gene Characterization Index, a bioinformatics method for scoring the extent to which a protein-encoding gene is functionally described. Inherently a reflection of human perception, the Gene Characterization Index is applied for
Danielle Kemmer +7 more
doaj +3 more sources
Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain. [PDF]
Genes (Basel), 2021 Camacho E +6 more
europepmc +3 more sources
Student biocuration projects as a learning environment [version 2; peer review: 2 approved]
F1000Research, 2022 Background: Bioinformatics is becoming an essential tool for the majority of biological and biomedical researchers. Although bioinformatics data is exploited by academic and industrial researchers, limited focus is on teaching this area to undergraduates,
Ruth C. Lovering +2 more
doaj +1 more source