SIMAP WS

SIMAP WS provides access to a pre-computed protein similarity matrix covering over 4 million amino acid sequences from public databases and completely sequenced genomes to support large-scale sequence similarity searches and protein functional analysis.

Key Features:

• Extensive Database Coverage: A pre-computed similarity matrix covers over 4 million amino acid sequences from public databases and completely sequenced genomes.
• Incremental Updates: The database and similarity matrix are maintained via incremental updates to incorporate new sequence data.
• Grid-Enabled Searches and Alignments: A grid-enabled software system performs sequence similarity searches and pairwise alignments using FASTA heuristics and the Smith-Waterman algorithm.
• ProtInfo Querying System: ProtInfo supports querying by complete sequences, sequence fragments, highly similar sequences, and title words.
• Pre-Calculated Features: Each sequence is supplemented with pre-calculated sequence-derived features from detailed sequence analyses.

Scientific Applications:

• Sequence Similarity Searches: Identify similar protein sequences across large datasets for comparative and evolutionary analyses.
• Pairwise Alignments: Generate precise pairwise alignments to detect conserved regions and functional motifs using Smith-Waterman.
• Functional Annotation: Infer potential protein functions by combining similarity data and pre-calculated sequence features.
• Data Integration: Integrate similarity and annotation data with other bioinformatics resources for downstream analyses.

Methodology:

SIMAP WS relies on a pre-computed protein similarity matrix maintained via incremental updates and uses a grid-enabled system to perform sequence similarity searches and pairwise alignments with FASTA heuristics and the Smith-Waterman algorithm; ProtInfo provides querying of complete sequences, fragments, highly similar sequences, and title words, and sequences include pre-calculated sequence-derived features.