AIMC Topic: Molecular Sequence Annotation
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The GOA database: gene Ontology annotation updates for 2015.
Nucleic acids research
Nov 6, 2014
The Gene Ontology Annotation (GOA) resource (http://www.ebi.ac.uk/GOA) provides evidence-based Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB). Manual annotations provided by UniProt curators are supplemented by ma...
Integrating GO and KEGG terms to characterize and predict acute myeloid leukemia-related genes.
Hematology (Amsterdam, Netherlands)
Oct 24, 2014
BACKGROUND/OBJECTIVE: Acute myeloid leukemia (AML) is a progressive and malignant cancer of myelogenous blood cells, which disturbs the production of normal blood cells. Although several risk and genetic factors (AML-related genes) have been investig...
DANN: a deep learning approach for annotating the pathogenicity of genetic variants.
Bioinformatics (Oxford, England)
Oct 22, 2014
UNLABELLED: Annotating genetic variants, especially non-coding variants, for the purpose of identifying pathogenic variants remains a challenge. Combined annotation-dependent depletion (CADD) is an algorithm designed to annotate both coding and non-c...
PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool.
Bioinformatics (Oxford, England)
Oct 1, 2014
UNLABELLED: Protein function prediction (PFP) is an automated function prediction method that predicts Gene Ontology (GO) annotations for a protein sequence using distantly related sequences and contextual associations of GO terms. Extended similarit...
DSSP 4: FAIR annotation of protein secondary structure.
Protein science : a publication of the Protein Society
Aug 1, 2025
Protein secondary structure annotation is essential for understanding protein architecture, serving as a cornerstone for structural classification, alignment, visualization, and machine learning applications. The Define Secondary Structure of Protein...
StructMAn 2.0 Web: a web server for structural annotation of protein sequences and mutations.
Nucleic acids research
Jul 7, 2025
StructMAn is a method for protein structural annotation. It describes each position of a protein sequence or specific variants in it in terms of their importance for the three-dimensional (3D) structure of the protein and its interactions with other ...
OntoTiger: a platform of ontology-based application tools for integrative biomedical exploration.
Nucleic acids research
Jul 7, 2025
Biomedical ontologies, such as Gene Ontology (GO), Disease Ontology (DO), and the Human Phenotype Ontology (HPO), have been extensively applied to characterize molecular roles and their semantic relationships in biomedical research and clinical pract...
GOReverseLookup: A gene ontology reverse lookup tool.
Computers in biology and medicine
Jun 1, 2025
BACKGROUND AND OBJECTIVE: The Gene Ontology (GO) project has been pivotal in providing a structured framework for characterizing genes and annotating them to specific biological concepts. While traditional gene annotation primarily focuses on mapping...
ChromActivity: integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types.
Genome biology
May 9, 2025
We introduce ChromActivity, a computational framework for predicting and annotating regulatory activity across the genome through integration of multiple epigenomic maps and various functional characterization datasets. ChromActivity generates genome...
argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO).
Bioinformatics (Oxford, England)
May 6, 2025
SUMMARY: Currently available and frequently used tools for annotating antibiotic resistance genes (ARGs) in genomes and metagenomes provide results using inconsistent nomenclature. This makes the comparison of different ARG annotation outputs challen...
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