PomBase Motif search

PomBase Motif search identifies occurrences of specified protein sequence motifs across the Schizosaccharomyces pombe (fission yeast) proteome to support inference of functional domains and regulatory elements.

Key Features:

• Comprehensive database access: Provides sequence information, molecular annotations, phenotypic details, and high-throughput study results from PomBase.
• Monthly data updates: PomBase content is updated monthly to reflect current annotations.
• Curated data quality: Manual curation by in-house curators and community researchers maintains high-quality annotations.
• Genome browser and comparative genomics: Accesses published high-throughput datasets via an integrated genome browser and includes genomic data for S. cryophilus, S. japonicus, and S. octosporus for comparative analyses.
• Proteome-wide motif scanning: Accepts user-specified motifs and scans the entire S. pombe proteome to identify motif occurrences.

Scientific Applications:

• Functional domain inference: Identification of motifs to infer protein functional domains.
• Protein–protein interaction prediction: Use of motif occurrences to predict potential interaction sites.
• Regulatory mechanism exploration: Exploration of sequence motifs associated with regulatory mechanisms at the molecular level.
• Comparative and evolutionary analyses: Comparative studies across S. cryophilus, S. japonicus, S. octosporus, and S. pombe.
• Support for basic and applied research: Facilitates investigations into cellular processes, disease mechanisms, and biotechnological applications.

Methodology:

Accepts user-defined motifs, scans PomBase protein sequences across the S. pombe proteome to identify motif occurrences, and returns lists of matching proteins, leveraging the comprehensive, manually curated PomBase dataset and available published high-throughput datasets via the integrated genome browser.