Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2002 Aug;15(8):643-9.
doi: 10.1093/protein/15.8.643.

Sequence Clustering Strategies Improve Remote Homology Recognitions While Reducing Search Times

Affiliations
Comparative Study

Sequence Clustering Strategies Improve Remote Homology Recognitions While Reducing Search Times

Weizhong Li et al. Protein Eng. .

Abstract

Sequence databases are rapidly growing, thereby increasing the coverage of protein sequence space, but this coverage is uneven because most sequencing efforts have concentrated on a small number of organisms. The resulting granularity of sequence space creates many problems for profile-based sequence comparison programs. In this paper, we suggest several strategies that address these problems, and at the same time speed up the searches for homologous proteins and improve the ability of profile methods to recognize distant homologies. One of our strategies combines database clustering, which removes highly redundant sequence, and a two-step PSI-BLAST (PDB-BLAST), which separates sequence spaces of profile composition and space of homology searching. The combination of these strategies improves distant homology recognitions by more than 100%, while using only 10% of the CPU time of the standard PSI-BLAST search. Another method, intermediate profile searches, allows for the exploration of additional search directions that are normally dominated by large protein sub-families within very diverse families. All methods are evaluated with a large fold-recognition benchmark.

Similar articles

See all similar articles

Cited by 22 articles

See all "Cited by" articles

Publication types

LinkOut - more resources

Feedback