An interactive tool for extracting exons and SNP from genomic sequence: isolation of HCN1 and HCN3 ion channel genes.
Genome Analyzer (GenoA) with a relational database back-end, was developed to extract information from mammalian genomic sequences. This data mining and visualization tool-set enables laboratory bench scientists to identify and assemble virtual cDNA from genomic exon sequences, and provides a starting point to identify potential alternative splice variants and polymorphisms in silico. The study described in this paper demonstrates the use of GenoA to study human brain hyperpolarization-activated cation channel genes HCN1 and HCN3.
Liu
Yuan
Y
Department of Bioinformatics, Merck & Co., Inc., WP53F-3001, West Point, PA 19486, USA. yuan_liu@merck.com
Wang
Yuhong
Y
Folander
Kimberly
K
Xie
Guochun
G
Blevins
Richard
R
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D054815:Cyclic Nucleotide-Gated Cation Channels; D004247:DNA / Q000235:genetics; D030541:Databases, Genetic; D005091:Exons; D023281:Genomics / Q000706:statistics & numerical data*; D006801:Humans; D064428:Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels; D007473:Ion Channels / Q000235:genetics*; D051379:Mice; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D015221:Potassium Channels / Q000235:genetics*; D051381:Rats; D016415:Sequence Alignment / Q000706:statistics & numerical data; D012985:Software Design
D054815:Cyclic Nucleotide-Gated Cation Channels; C578665:HCN1 protein, human; C472018:HCN3 protein, human; C578666:Hcn1 protein, mouse; C578667:Hcn1 protein, rat; D064428:Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels; D007473:Ion Channels; D009419:Nerve Tissue Proteins; D015221:Potassium Channels; D004247:DNA