A genetic algorithm for designing gene family-specific oligonucleotide sets used for hybridization: the G protein-coupled receptor protein superfamily.
BACKGROUND
Massive oligonucleotide hybridization is one of the most promising technologies of functional genome analysis. The critical point is to design appropriate sets of oligonucleotides that can be used effectively in identification by hybridization.


RESULTS
Using a genetic algorithm approach, we have attempted to design sets of oligo probes capable of identifying new genes belonging to a defined gene family within a cDNA or genomic library. It is not limited by oligonucleotide length and admits the letter 'N' in the structure of the oligonucleotides selected. One of the major advantages of this approach is the low homology required to identify functional families of sequences with little homology. We have designed the oligonucleotide sets that are most selective for the cDNA clones of transmembrane G protein-coupled receptors (GPCRs), a large family of proteins that form part of a modular system of extracellular signal transduction to the intracellular second messenger pathways. The accuracy of identification has been checked on the EST library containing 713 870 cDNA sequences. A set of 15 oligos between 7 and 14 bases in length has correctly identified 70% of the GPCR cDNA collection sequences with 0.02% false positives.


BACKGROUND
The developed software is available by ftp://ftp.bionet.nsc. ru/pub/biology/ and on the Web page http://www.bionet.nsc. ru/SRCG/Oligoselector/.


BACKGROUND
kel@.bionet.nsc.ru; sebastian. meier-ewert@gpc-ag.com
Kel
A
A
Institute of Cytology and Genetics, pr.Lavrentyeva 10, 630090, Novosibirsk, Russia. kel@bionet.nsc.ru
Ptitsyn
A
A
Babenko
V
V
Meier-Ewert
S
S
Lehrach
H
H
D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D017931:DNA Primers / Q000235:genetics*; D019204:GTP-Binding Proteins / Q000378:metabolism; D006801:Humans; D008957:Models, Genetic; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D009693:Nucleic Acid Hybridization / Q000235:genetics; D011956:Receptors, Cell Surface / Q000235:genetics*; D018179:Receptors, Thrombin / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods; D012689:Sequence Homology, Nucleic Acid; D015398:Signal Transduction / Q000235:genetics; D012986:Software Validation
D017931:DNA Primers; D011956:Receptors, Cell Surface; D018179:Receptors, Thrombin; D019204:GTP-Binding Proteins