GWIPS-viz

GWIPS-viz visualizes genomic alignments of ribosome profiling (ribo-seq) and mRNA-seq data in a UCSC Genome Browser framework to enable analysis of ribosome density and translation initiation sites across multiple genomes.

Key Features:

• Integration of ribo-seq and mRNA-seq data: Provides ribo-seq and mRNA-seq alignment tracks alongside annotation tracks for genomes including human, mouse, zebrafish, nematode, yeast, bacteria (Escherichia coli K12 and Bacillus subtilis), human cytomegalovirus, and bacteriophage lambda to quantify ribosome density along mRNA transcripts.
• Cross-species and cross-study comparisons: Offers separate tracks for each ribo-seq study and supports comparison of orthologous genes across species to assess reproducibility and variation in ribosome densities.
• Translation initiation site (TIS) exploration: Enables examination of AUG and non-AUG TISs and the resulting alternative or heterogeneous N-termini that affect proteoform diversity and coding sequence boundary definitions.
• UCSC Genome Browser framework: Built upon the UCSC Genome Browser infrastructure to display genomic alignments and annotation tracks within a genome-browser environment.

Scientific Applications:

• In vivo protein synthesis analysis: Study genome-wide ribosome occupancy and translation dynamics across diverse organisms.
• Gene expression and translational control studies: Investigate regulation of translation and mechanisms affecting ribosome distribution on mRNAs.
• Alternative initiation and proteoform characterization: Identify and evaluate effects of alternative AUG and non-AUG initiation on proteoform N-termini and coding sequence boundaries.
• Comparative and evolutionary analysis: Compare ribosome profiling data across studies and species to assess conservation and variability in protein synthesis.

Methodology:

Displays genomic alignments of ribo-seq reads alongside mRNA-seq controls and annotation tracks, provides separate tracks per ribo-seq study, and reports ribosome density along mRNA transcripts within the UCSC Genome Browser framework.