UNIT 2.2 Using the Blocks Database to Recognize Functional Domains

  1. Jorja G. Henikoff1,
  2. Elizabeth A. Greene1,
  3. Nick Taylor1,
  4. Steven Henikoff1,
  5. Shmuel Pietrokovski2

Published Online: 1 AUG 2002

DOI: 10.1002/0471250953.bi0202s00

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Henikoff, J. G., Greene, E. A., Taylor, N., Henikoff, S. and Pietrokovski, S. 2002. Using the Blocks Database to Recognize Functional Domains. Current Protocols in Bioinformatics. 00:2.2:2.2.1–2.2.32.

Author Information

  1. 1

    Fred Hutchinson Cancer Research Center, Seattle, Washington

  2. 2

    Weizmann Institute of Science, Rehovot, Israel

Publication History

  1. Published Online: 1 AUG 2002
  2. Published Print: JAN 2003


Blocks are ungapped multiple alignments of related protein sequence segments that correspond to the most conserved regions of the proteins. The Blocks Database is a collection of blocks representing known protein families that can be used to compare a protein or DNA sequence with documented families of proteins. Protocols in this unit describe the analysis of proteins and families using Blocks-based tools, including searching, exploring relationships with trees, making new blocks, and designing PCR primers from blocks for isolating homologous sequences.