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
. 2000 Apr;10(4):543-6.
doi: 10.1101/gr.10.4.543.

Drosophila genomic sequence annotation using the BLOCKS+ database

J G Henikoff  1 , S Henikoff
Affiliations

Drosophila genomic sequence annotation using the BLOCKS+ database

J G Henikoff et al. Genome Res. 2000 Apr.

Abstract

A simple and general homology-based method for gene finding was applied to the 2.9-Mb Drosophila melanogaster Adh region, the target sequence of the Genome Annotation Assessment Project (GASP). Each strand of the entire sequence was used as query of the BLOCKS+ database of conserved regions of proteins. This led to functional assignments for more than one-third of the genes and two-thirds of the transposons. Considering the enormous size of the query, the fact that only two false-positive matches were reported emphasizes the high selectivity of protein family-based methods for gene finding. We used the search results to improve BLOCKS+ by identifying compositionally biased blocks. Our results confirm that protein family databases can be used effectively in automated sequence annotation efforts.

PubMed Disclaimer

Comment in

References

    1. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF, Kerlavage AR, McCombie WR, Venter JC. Complementary DNA sequencing: Expressed sequence tags and human genome project. Science. 1991;252:1651–1656. - PubMed
    1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–410. - PubMed
    1. Ashburner M, Misra S, Roote J, Lewis SE, Blazej R, Davis T, Doyle C, Galle R, George R, Harris N, Hartzell G, Harvey D, Hong L, Houston K. An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region. Genetics. 1999;153:179–219. - PMC - PubMed
    1. Attwood TK, Flower DR, Lewis AP, Mabey JE, Morgan SR, Scordis P, Selley JN, Wright W. PRINTS prepares for the new millenium. Nucleic Acids Res. 1999;27:220–225. - PMC - PubMed
    1. Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, Sonnhammer ELL. Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res. 1999;27:260–262. - PMC - PubMed

Publication types

Substances

LinkOut - more resources