Design of long oligonucleotide probes for functional gene detection in a microbial community.
BACKGROUND
Analysis of the functions of microorganisms and their dynamics in the environment is essential for understanding microbial ecology. For analysis of highly similar sequences of a functional gene family using microarrays, the previous long oligonucleotide probe design strategies have not been useful in generating probes.


RESULTS
We developed a Hierarchical Probe Design (HPD) program that designs both sequence-specific probes and hierarchical cluster-specific probes from sequences of a conserved functional gene based on the clustering tree of the genes, specifically for analyses of functional gene diversity in environmental samples. HPD was tested on datasets for the nirS and pmoA genes. Our results showed that HPD generated more sequence-specific probes than several popular oligonucleotide design programs. With a combination of sequence-specific and cluster-specific probes, HPD generated a probe set covering all the sequences of each test set.


BACKGROUND
http://brcapp.kribb.re.kr/HPD/
Chung
Won-Hyong
WH
Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon.
Rhee
Sung-Keun
SK
Wan
Xiu-Feng
XF
Bae
Jin-Woo
JW
Quan
Zhe-Xue
ZX
Park
Yong-Ha
YH
D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D017931:DNA Primers / Q000737:chemistry*; D015342:DNA Probes / Q000737:chemistry; D004463:Ecology / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods*; D005798:Genes, Bacterial; D005821:Genetic Techniques; D014644:Genetic Variation; D016680:Genome, Bacterial; D020407:Internet; D008957:Models, Genetic; D008962:Models, Theoretical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D015345:Oligonucleotide Probes / Q000235:genetics; D011381:Programming Languages; D012984:Software
D017931:DNA Primers; D015342:DNA Probes; D015345:Oligonucleotide Probes