Globin gene server: a prototype E-mail database server featuring extensive multiple alignments and data compilation for electronic genetic analysis.
The sequence of virtually the entire cluster of beta-like globin genes has been determined from several mammals, and many regulatory regions have been analyzed by mutagenesis, functional assays, and nuclear protein binding studies. This very large amount of sequence and functional data needs to be compiled in a readily accessible and usable manner to optimize data analysis, hypothesis testing, and model building. We report a Globin Gene Server that will provide this service in a constantly updated manner when fully implemented. The Server has two principal functions. The first (currently available) provides an annotated multiple alignment of the DNA sequences throughout the gene cluster from representatives of all species analyzed. The second compiles data on functional and protein binding assays throughout the gene cluster. A prototype of this compilation using the aligned 5' flanking region of beta-globin genes from five species shows examples of (1) well-conserved regions that have demonstrated functions, including cases in which the functional data are in apparent conflict, (2) proposed functional regions that are not well conserved, and (3) conserved regions with no currently assigned function. Such an electronic genetic analysis leads to many readily testable hypotheses that were not immediately apparent without the multiple alignment and compilation. The Server is accessible via E-mail on computer networks, and printed results can be obtained by request to the authors. This prototype will be a helpful guide for developing similar tools for many genomic loci.
Hardison
R
R
Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park 16802.
Chao
K M
KM
Schwartz
S
S
Stojanovic
N
N
Ganetsky
M
M
Miller
W
W
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000378:metabolism; D016208:Databases, Factual; D005701:Galago / Q000235:genetics; D005914:Globins / Q000235:genetics*; D006041:Goats / Q000235:genetics; D015186:Hominidae / Q000235:genetics*; D006801:Humans; D008322:Mammals / Q000235:genetics*; D051379:Mice / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family; D016296:Mutagenesis; D009816:Office Automation; D011817:Rabbits / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid; D012689:Sequence Homology, Nucleic Acid
D004268:DNA-Binding Proteins; D005914:Globins