Article thumbnail
Location of Repository

CORAL: aligning conserved core regions across domain families

By Jessica H. Fong and Aron Marchler-Bauer


Motivation: Homologous protein families share highly conserved sequence and structure regions that are frequent targets for comparative analysis of related proteins and families. Many protein families, such as the curated domain families in the Conserved Domain Database (CDD), exhibit similar structural cores. To improve accuracy in aligning such protein families, we propose a profile–profile method CORAL that aligns individual core regions as gap-free units

Topics: Original Papers
Publisher: Oxford University Press
OAI identifier:
Provided by: PubMed Central

Suggested articles


  1. (2004). A comparison of scoring functions for protein sequence profile alignment.
  2. (2005). A structure-based method for protein sequence alignment.
  3. Altschul,S.F.etal.(1997)GappedBLASTandPSI-BLAST:anewgenerationofprotein database search programs.
  4. (2002). CDD: a database of conserved domain alignments with links to domain three-dimensional structure.
  5. (2000). Comparison of sequence profiles. Strategies for structural predictions using sequence information.
  6. (2003). COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance.
  7. (2001). Consistency analysis of similarity between multiple alignments: prediction of protein function and fold structure from analysis of local sequence motifs.
  8. (2003). Finding weak similarities between proteins by sequence profile comparison.
  9. (1981). Identification of common molecular subsequences.
  10. (2001). Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.
  11. (2000). Increased coverage of protein families with the blocks database servers.
  12. (2000). Large-scale comparison of protein sequence alignment algorithms with structure alignments.
  13. (1990). Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.
  14. (1993). Optimal alignment between groups of sequences and its application to multiple sequence alignment.
  15. (2006). Pfam: clans, web tools and services.
  16. (2001). Picasso: generating a covering set of protein family profiles.
  17. (2003). Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments.
  18. (2004). Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods.
  19. (2005). ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins.
  20. (2005). Protein homology detection by HMM-HMM comparison.
  21. (2006). Refining multiple sequence alignments with conserved core regions.
  22. (2005). SABmark–a benchmark for sequence alignment that covers the entire known fold space.
  23. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures.
  24. (1996). Searching databases of conserved sequence regions by aligning protein multiple-alignments.
  25. (2006). SMART 5: domains in the context of genomes and networks.
  26. (1996). Surprising similarities in structure comparison.
  27. (2007). The identification of complete domains within protein sequences using accurate E-values for semi-global alignment.
  28. (2007). The SUPERFAMILY database in 2007: families and functions.
  29. (1995). Threading a database of protein cores.
  30. (2002). Within the twilight zone: a sensitive profile-profile comparison tool based on information theory.

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.