A new annotation file format based on JSON, containing all information stored in the GenBank format but with advantageoius parsing and information structure properties.

Predicting Alzheimer’s disease risk factors from the variant fingerprints of non-AD genes

A toolkit for identifying gene homologs in closely related species.

A comprehensive microbial genomic analysis pipeline that includes quality control, gene prediction, annotation, and comparative genomic analysis for identifying and visualizing key genetic features in microbial genomes.

Nextflow workflow to generate gene track files for HiGlass

Linux tool for relative mutation rate of different genes across viral strains.

Command-line tool for retrieving and logging human gene annotations from MyGene.info

Analysis workflow to generate fungal assemblies, generate gene structural and functional annotations

A bioinformatics software system designed for comparing gene annotations between different releases for a selected species. It includes Python classes for data processing, information extraction, a MySQL relational database, and web-based interfaces for dynamic data querying.

Supplementary code for the paper: Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders

EMBLish aims to provide a tool for converting gene prediction files such as Maker output file and gene annotation files such as Pannzer2 output file into the EMBL format

A NextFlow pipeline for the annotation of gene homologs using SABAT.

GTF/GFF per gene non-overlapping exon length calculator

Stone Lab @ CSUEB Collaboration Projects focused on Plant Bioinformatics

This is a recipe to make my gene matrix

Python tool for relative mutation rate of different genes across viral strains.

Analysis of different versions of Platypus Gene Annotations from the Ensembl database. Includes a basic frontend to present data, hosted using a Miami class server. The backend is a database containing gene data that a user can query through the frontend.

high-performance BED-to-GTF converter written in Rust

Command line tools for working with various gene annotation formats.

A layered view of gene annotation.