ProRepeat

ProRepeat provides a curated repository and analytical resource for identification, cataloging, and analysis of amino acid tandem repeats in proteins by integrating repeat sequences from UniProt and 85 fully sequenced eukaryotic proteomes from RefSeq.

Key Features:

• Database integration: Integrates repeat sequences from all proteins in the UniProt knowledgebase and 85 fully sequenced eukaryotic proteomes from the RefSeq collection.
• Repeat types cataloged: Catalogs non-redundant perfect tandem repeats, approximate tandem repeats, and simple low-complexity sequences.
• Query and filtering: Supports querying and filtering by repeat unit length, repeat copy number, repeat position within protein sequences, UniProt entry ID, protein description, sequence length, gene name, and taxonomy.
• Positional bias analysis: Detects positional biases of repeats, exemplified by leucine repeats enriched at the N-terminus of eukaryotic protein sequences.
• Comparative proteome analysis: Enables comparative analyses of repeat abundance and patterns across different proteomes.
• Functional and codon-level analyses: Facilitates investigation of protein functional classifications associated with repeats and examines GC content constraints of codons encoding tandem repeats.

Scientific Applications:

• Distribution and bias characterization: Characterize distribution and positional bias of amino acid tandem repeats across UniProt and 85 RefSeq eukaryotic proteomes.
• Comparative proteomics: Compare repeat abundance and patterns across multiple eukaryotic proteomes.
• Function–repeat association: Investigate associations between tandem repeats and protein functional classifications.
• Codon and GC-content analysis: Assess GC content constraints related to codons corresponding to tandem repeats.

Methodology:

Integrates repeat sequences from UniProt and 85 RefSeq eukaryotic proteomes and identifies and catalogs non-redundant perfect tandem repeats, approximate tandem repeats, and simple low-complexity sequences.