Increased coverage of protein families with the Blocks Database servers

Jorja G. Henikoff

doi:10.1093/nar/28.1.228

January 1, 2000Nucleic Acids ResearchOpen Access

Increased coverage of protein families with the Blocks Database servers

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Key Points

To describe major updates to the Blocks Database web and email servers designed to broaden sequence coverage and enhance functional annotation tools for protein families.
Integrated protein family alignments from the Pfam-A, ProDom, and Domo databases alongside existing PROSITE and PRINTS collections to create the expanded Blocks+ Database.
Incorporated NCBI's IMPALA search program, updated Block Searcher statistical scoring algorithms, and added capabilities for displaying blocks on Protein Data Bank (PDB) structures.
Nearly doubled the total number of curated protein families available for searching compared to previous database releases.
Enabled interactive three-dimensional mapping of conserved multiple alignment blocks directly onto corresponding PDB macromolecular structures.

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Implication

Database update reports expanded coverage of conserved protein families across multiple alignment repositories, highlighting improved sequence search sensitivity and structural visualization.

Abstract

The Blocks Database WWW (http://blocks.fhcrc.org ) and Email (blocks@blocks.fhcrc.org ) servers provide tools to search DNA and protein queries against the Blocks+ Database of multiple alignments, which represent conserved protein regions. Blocks+ nearly doubles the number of protein families included in the database by adding families from the Pfam-A, ProDom and Domo databases to those from PROSITE and PRINTS. Other new features include improved Block Searcher statistics, searching with NCBI's IMPALA program and 3D display of blocks on PDB structures.

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Jorja G. Henikoff (2000) studied this question.

synapsesocial.com/papers/6a113f30c642e492e4dd8d28 https://doi.org/10.1093/nar/28.1.228

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Increased coverage of protein families with the Blocks Database servers

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Increased coverage of protein families with the Blocks Database servers

Key Points

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