GCView

GCView analyzes genomic context surrounding query proteins to identify neighboring protein-coding genes, infer operon structures, and compare evolutionary relationships using protein homology search results such as BLASTp.

Key Features:

• Input from homology searches: Accepts input from one or multiple protein homology searches, for example BLASTp results.
• Genomic neighborhood annotation: Annotates neighboring protein-coding genes and labels regions of homology for each hit.
• Iterative refinement: Supports adding additional searches to iteratively refine the analysis output.
• Comparative grouping: Groups outputs by hits for different proteins to enable comparison of operon compositions and structures.
• Integration with MPI Bioinformatics Toolkit: Accepts forwarded results from homology search tools within the MPI Bioinformatics Toolkit for downstream sequence analyses.

Scientific Applications:

• Operon structure analysis: Examination of operons as whole entities to detect changes in composition and arrangement of protein-coding genes.
• Evolutionary genomics: Comparison of genomic neighborhoods across species or datasets to infer evolutionary relationships of proteins and operons.
• Functional gene-neighborhood analysis: Identification of conserved neighboring genes to generate hypotheses about gene function and regulation.

Methodology:

Accepts one or multiple protein homology search results (e.g., BLASTp); annotates neighboring protein-coding genes and regions of homology for each hit; groups outputs by hits for different proteins; allows adding further searches to iteratively refine outputs; accepts forwarded results from homology search tools within the MPI Bioinformatics Toolkit.