functional-annotation

A pipeline to go from raw sequencing data to high quality bins and pretty plots.

A multi-way annotator for genetic elements and genetic variations

A repository for the development of patterns and terms for axiomatisation and refactoring of the GO MF branch

Python3 extension for DAVID Bioinformatics Tool

Package for improving the functional annotation of bacterial genomes, classification of protein-coding sequences into clusters of orthologous groups, and visualization of the final annotated genome.

Snakemake pipeline to benchmark 11 functional pathway annotation systems

Knowles Lab Research: determine which genetic variants cause a phenotype with non-binary functional annotations

ncRNA identification, annotation and functional prediction

A computational tools for improving the functional annotation of bacterial genomes and the classification of CDSs into cllusters of orthologous groups (COGs). It allows summarizing annotations from different resources to provide a more accurate annotation of genes regarding their assignment into COGs and their categories.

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

Exploratory Framework for Genotype-Phenotype Prediction

UniProt Id Mapping through API

GWAS locus visualization and functional annotation workflows for variant interpretation.

An epigenome-wide association study (EWAS) pipeline profiling DNA methylation (5mC) dynamics across post-mortem Alzheimer's brain regions. Investigates cell-type-specific differential methylation and chromatin accessibility correlations, utilizing OLS with robust standard errors and machine learning biomarker panel classification.

ATLAS - Three commands to start analyzing your metagenome data

Synthetic Python demo for annotating mock gene lists with UniProt-style functional and GO-term summaries.

Multi-dimensional Annotation Class Integrative Estimation

Fast genome-wide functional annotation through orthology assignment

Bakta and Prokka call the same 87,859 CDS regions in 25 complete bacterial genomes, then give 51.7% of them different product names. Both wrap Prodigal, so they agree on gene boundaries and diverge on function. Grouped-by-genome ML shows the disagreement tracks database coverage, not sequence.

A reproducible modern re-analysis of the O67940_AQUAE protein-function case study, rebuilding the evidence chain behind annotation transfer with current databases, AlphaFold, structural comparison, residue mapping, provenance tracking, and explicit limits on what the computational workflow can and cannot prove.