Seq2Ref

Seq2Ref identifies and ranks experimentally characterized and manually curated reference proteins to improve functional interpretation of protein sequences derived from genome sequencing by evaluating homologous relationships.

Key Features:

• BLAST integration: Uses the Basic Local Alignment Search Tool (BLAST) to identify homologous proteins to a query sequence.
• Identification of reference proteins: Detects reference proteins that are experimentally characterized or manually curated among BLAST results.
• Publication reporting: Links identified reference proteins to publications that describe their experimental characterization.
• Plurality-based rating system: Applies a plurality-based rating to evaluate homologous relationships and rank the relevance of reference proteins to the query.

Scientific Applications:

• Functional annotation of uncharacterized proteins: Facilitates transfer of experimentally supported functional information to uncharacterized protein sequences.
• Large-scale dataset interpretation: Supports prioritization and interpretation of protein sequences in large genomic and proteomic datasets.
• Support for genomics, proteomics, and systems biology: Provides experimentally grounded reference links useful for hypothesis generation and system-level analyses.

Methodology:

Sequence querying of a protein sequence is followed by BLAST searches to find homologous sequences; experimentally characterized or manually curated reference proteins are identified among BLAST hits; a plurality-based rating system ranks reference relevance; and reference proteins are linked to publications reporting their experimental characterizations.