Blocks WWW Server

Blocks WWW Server performs searches of DNA and protein sequences against the Blocks+ database of conserved multiple alignments to support sequence classification, functional prediction, and evolutionary analysis.

Key Features:

• Blocks+ database: a compendium of multiple alignments representing conserved protein regions used for functional and evolutionary inference.
• Database integration: merges entries from Prosite, Prints, Pfam-A, ProDom, and Domo into a unified resource.
• Coverage: contains 1995 protein families represented by 8909 blocks, approximately doubling the coverage of the predecessor database.
• Scoring model: construction and sequence classification leverage the PROTOMAT/BLOSUM scoring model.
• Blocks-versus-blocks searching (LAMA): performs non-redundant hierarchical compilation and identifies overlapping protein families to minimize redundancy.
• Family discrimination: distinguishes related but distinct families such as SNF2 ATPases versus other helicases or ATPases.
• Sequence queries: supports querying both DNA and protein sequences against the Blocks+ Database.
• Search statistics: provides improved Block Searcher statistics that report detailed search-result metrics.
• IMPALA integration: supports integration with NCBI's IMPALA program for enhanced searching capabilities.
• 3D mapping: maps blocks onto PDB structures for three-dimensional visualization of conserved regions.

Scientific Applications:

• Sequence classification: assigns query sequences to protein families based on conserved multiple alignments.
• Functional prediction: infers molecular function from conserved blocks within protein families.
• Evolutionary studies: analyzes conserved regions across proteins to investigate evolutionary relationships.
• Structural biology: maps conserved blocks onto PDB structures to relate sequence conservation to three-dimensional architecture.
• Molecular function analysis: examines conserved motifs and blocks to interpret biochemical activity and functional sites.
• Family delineation: identifies and distinguishes overlapping or related protein families, such as SNF2 ATPases versus other helicases/ATPases.

Methodology:

Blocks+ was constructed by integrating Prosite, Prints, Pfam-A, ProDom, and Domo and uses the PROTOMAT/BLOSUM scoring model; LAMA performs blocks-versus-blocks non-redundant hierarchical compilation; searches generate Block Searcher statistics, can integrate NCBI's IMPALA, and blocks can be mapped onto PDB structures for 3D visualization.