COMPASS

COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. We present a novel method for the comparison of multiple protein alignments with assessment of statistical significance (COMPASS). The method derives numerical profiles from alignments, constructs optimal local profile-profile alignments and analytically estimates E-values for the detected similarities. The scoring system and E-value calculation are based on a generalization of the PSI-BLAST approach to profile-sequence comparison, which is adapted for the profile-profile case. Tested along with existing methods for profile-sequence (PSI-BLAST) and profile-profile (prof_sim) comparison, COMPASS shows increased abilities for sensitive and selective detection of remote sequence similarities, as well as improved quality of local alignments. The method allows prediction of relationships between protein families in the PFAM database beyond the range of conventional methods. Two predicted relations with high significance are similarities between various Rossmann-type folds and between various helix-turn-helix-containing families. The potential value of COMPASS for structure/function predictions is illustrated by the detection of an intricate homology between the DNA-binding domain of the CTF/NFI family and the MH1 domain of the Smad family.


References in zbMATH (referenced in 9 articles )

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  1. Keith, Jonathan M. (ed.): Bioinformatics. Volume II: structure, function, and applications (2017)
  2. Gullotto, Danilo; Nolassi, Mario Salvatore; Bernini, Andrea; Spiga, Ottavia; Niccolai, Neri: Probing the protein space for extending the detection of weak homology folds (2013)
  3. Margelevicius, Mindaugas; Venclovas, Ceslovas: Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison (2010) ioport
  4. Poleksic, Aleksandar: Island method for estimating the statistical significance of profile-profile alignment scores (2009) ioport
  5. Sadreyev, Ruslan; Tang, Ming; Kim, Bong-Hyun; Grishin, Nick V.: COMPASS server for homology detection: improved statistical accuracy, speed and functionality (2009) ioport
  6. Sadreyev, Ruslan; Wang, Yong; Grishin, Nick V.: Considering scores between unrelated proteins in the search database improves profile comparison (2009) ioport
  7. Boekhorst, Jos; Snel, Berend: Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties (2007) ioport
  8. Sadreyev, Ruslan; Tang, Ming; Kim, Bong-Hyun; Grishin, Nick V.: COMPASS server for remote homology inference. (2007) ioport
  9. Hung, Chun-Min; Huang, Yueh-Min; Chang, Ming-Shi: Alignment using genetic programming with causal trees for identification of protein functions (2006)