GIMP (Gene Information Mining Pipeline) -- Tools for gene data collection, integration, selection and preparation for association study on complex diseases. It serves both candidate gene-based approach and positional cloning-based approach.
Human data (Genome, Gene, and SNP) only!
Some tools will work for studies of the other species, if you do not need to use data provided by our systems, including genome sequence, SNPs, etc.
Existing
web sites for gene/SNP query
Batch query for candidate genes
Search for gene map position, gDNA size, mRNA Genbank accession numbers, expression tissues, OMIM reported diseases. Expression tissues can be filtered.
Search for genes mapped to certain genomic regions.
Batch query for
conserved genomic regions
Search for conserved genomic regions among human, chimp, mouse, rat, and chicken.
Search for exons or promoters that are not conserved by comparing HomoPhyloQuery results and gene exons data.
Please cite the references:
Chunyu Liu, Tu Nguyen, Ruifang Zhang, Fengxia Yao, Zanhua Zhu, Elliot S. Gershon. SNP Information Mining Pipeline (SIMP) for Complex Disease Studies. 53rd Annual Meeting of the American Society of Human Genetics. Los Angeles, CA, 4-8, November. Am J Human Genet 73(5):421. abstract# 1470.
Chunyu Liu, Tom I. Bonner, Tu Nguyen, Jennifer L. Lyons, Susan L. Christian, Elliot S. Gershon. DNannotator: annotation software tool kit for regional genomic sequences. Nucleic Acids Res. 2003. 31(13):3729-3735
Tu Nguyen, Chunyu Liu, Elliot S. Gershon, Francis J. McMahon. Frequency Finder: A multi-source web application for collection of public allele frequencies of SNP markers. Bioinformatics. 2004. 20(3):439–443
8/16/2004 updated
