SNP ID-info: SNP ID searching and visualization platform.
Many association studies provide the relationship between single nucleotide polymorphisms (SNPs), diseases and cancers, without giving a SNP ID, however. Here, we developed the SNP ID-info freeware to provide the SNP IDs within inputting genetic and physical information of genomes. The program provides an "SNP-ePCR" function to generate the full-sequence using primers and template inputs. In "SNPosition," sequence from SNP-ePCR or direct input is fed to match the SNP IDs from SNP fasta-sequence. In "SNP search" and "SNP fasta" function, information of SNPs within the cytogenetic band, contig position, and keyword input are acceptable. Finally, the SNP ID neighboring environment for inputs is completely visualized in the order of contig position and marked with SNP and flanking hits. The SNP identification problems inherent in NCBI SNP BLAST are also avoided. In conclusion, the SNP ID-info provides a visualized SNP ID environment for multiple inputs and assists systematic SNP association studies. The server and user manual are available at http://bio.kuas.edu.tw/snpid-info.
Yang
Cheng-Hong
CH
Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Taiwan, ROC.
Chuang
Li-Yeh
LY
Cheng
Yu-Huei
YH
Wen
Cheng-Hao
CH
Chang
Phei-Lang
PL
Chang
Hsueh-Wei
HW
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D030541:Databases, Genetic; D006801:Humans; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software; D014584:User-Computer Interface