Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 1998 Jan 1;26(1):309-12.
doi: 10.1093/nar/26.1.309.

Superior performance in protein homology detection with the Blocks Database servers

S Henikoff  1 , S Pietrokovski, J G Henikoff
Affiliations

Superior performance in protein homology detection with the Blocks Database servers

S Henikoff et al. Nucleic Acids Res. .

Abstract

The Blocks Database World Wide Web (http://www.blocks.fhcrc.org ) and Email (blocks@blocks.fhcrc.org) servers provide tools for the detection and analysis of protein homology based on alignment blocks representing conserved regions of proteins. During the past year, searching has been augmented by supplementation of the Blocks Database with blocks from the Prints Database, for a total of 4754 blocks from 1163 families. Blocks from both the Blocks and Prints Databases and blocks that are constructed from sequences submitted to Block Maker can be used for blocks-versus-blocks searching of these databases with LAMA, and for viewing logos and bootstrap trees. Sensitive searches of up-to-date protein sequence databanks are carried out via direct links to the MAST server using position-specific scoring matrices and to the BLAST and PSI-BLAST servers using consensus-embedded sequence queries. Utilizing the trypsin family to evaluate performance, we illustrate the superiority of blocks-based tools over expert pairwise searching or Hidden Markov Models.

PubMed Disclaimer

References

    1. Curr Opin Struct Biol. 1996 Jun;6(3):361-5 - PubMed
    1. Nucleic Acids Res. 1996 Oct 1;24(19):3836-45 - PubMed
    1. Trends Biochem Sci. 1996 Nov;21(11):444-5 - PubMed
    1. Nucleic Acids Res. 1997 Jan 1;25(1):212-7 - PubMed
    1. Nucleic Acids Res. 1997 Jan 1;25(1):217-21 - PubMed

Publication types