GlyXYMuster

GlyXYMuster is a bioinformatics toolkit designed to identify and characterize Gly-X-Y repeats in protein sequences, with a focus on collagen-like proteins that adopt a triple-helical structure. The Gly-X-Y motif refers to a repeating tripeptide pattern in which glycine appears at every third position, commonly represented as Gly-X-Y, where X and Y are variable residues that often include proline and hydroxyproline. The project provides an integrated workflow for detecting these patterns, annotating them within protein sequences, and summarizing their distribution across datasets.

Key capabilities include sequence scanning for Gly-X-Y tripeptides, reporting the number, start and end positions, and periodicity of repeats; generating summary statistics and visualizations such as repeat-length histograms and per-sequence motif maps; exporting results in standard formats (FASTA, CSV, GFF3); and linking motifs to known domains and structural data when available. The software emphasizes reproducibility, supports batch processing, and can be extended with custom motif definitions.

Implementation and availability: GlyXYMuster is implemented in Python with optional R components for advanced visualization. It operates as a command-line tool and as a Python library and is distributed under an open-source license. The project began in 2021 as a collaborative effort among computational biologists to standardize reporting of Gly-X-Y repeats and to facilitate studies of collagen evolution and assembly. Documentation, example datasets, and the codebase are hosted on a public repository, with ongoing updates and community contributions.

See also: Collagen; Gly-X-Y repeats; protein motifs.