Affyrmation: Affymetrix SNP Chip Marker Affirmation
The system performs real-time Affymetrix SNP Information Affirmation among NCBI, UCSC and SNPper websites, and supports batch processing by uploading a file. The result can be presented in either HTML or MS Excel format.
Chen, Y.H., Tsai, M.F. and Yao, A. (2006) Affyrmation: Online Real-time Affirmation and Annotation for Affymetrix SNP Information, JOURNAL OF GENETICS AND MOLECULAR BIOLOGY PDF

QualiSeq: Quality Genomic Sequence Retrieval
The system retrieves the region around an SNP(rs#) / basepair or region between two SNPs / basepairs from Ensembl, NCBI and UCSC. It also compares the sequences and shows you the similarity between any two sources. You can download the sequences(FASTA) and alignments from result page. The system also checks the sequence quality.It compares the order of STS markers on the TNG map with the Physical map. It also gets the segmental duplicates from UCSC.
Yu-Chang Cheng, Tz-Chao Lin, Kuo-His Lee, Yan-Hau Chen, Ming-Fang Tsai, Yi-Jung Lin, and Adam Yao (2006) Qualiseq: Quality Genomic Sequence Retrieval, JOURNAL OF GENETICS AND MOLECULAR BIOLOGY PDF

GenoWatch: A Disease Gene Mining Browser For Association Study
GenoWatch can efficiently extract up-to-date information about multiple markers and their associated genes in batch mode from many relevant biological databases in real-time. The comprehensive gene information retrieved includes gene ontology, function, pathway, disease, related articles in PubMed and so on. Subsequent SNP functional impact analysis and primer design of a target gene for re-sequencing can also be done in a few clicks. The presentation of results has been carefully designed to be as intuitive as possible to all users.
Chen, Y.H., Liu, C.K., Chang, S.C., Lin, Y.J., Tsai, M.F., Chen, Y.T. and Yao, Adam (2008) GenoWatch: a disease gene mining browser for association study, Nucleic Acids Research, doi:10.1093/nar/gkn214 Full Text

VisualSNP: Robust Functional SNP Prioritization Tool
Function Analysis and Selection Tool for SNP association studies. It can accelerate your SNP selection process by candidate genes approach, and provide function prediction of SNP impacts on DNA trascription, pre-mRNA alternative splicing, and protein structure which helps you identify SNP most likely to have functional effects for genotyping.
(in preparation)

PrimerZ: Streamlining Primer Design for Genes and SNPs
The system allows the researchers choose the genes of interest for primer design in either the human, or mouse genomes. The regions can be identified by the gene name, or Ensembl accession. Sequence and exon information is fetched from the ensembl database. The program used to design primers is the Primer3 software.
Tsai, M.F., Lin, Y.J., Cheng, Y.C., Lee, K.H., Huang, C.C., Chen, Y.T. and Yao, Adam (2007) PrimerZ: streamlined primer design for promoters, exons and human SNPs, Nucleic Acids Research, doi:10.1093/nar/gkm383 Full Text