NCBI genome build 37.2
dbSNP build 132

genewindow.v3

The Genewindow web-site is the primary tool for pre- and post-genetic bioinformatics and analytical work at the Core Genotyping Facility (CGF) at the National Cancer Institute, which is currently analyzing approximately 75,000 samples at a rate of four million SNP genotypes per year. While Genewindow is implemented for the human genome and integrated with the CGF laboratory data, it stands as a useful tool to assist investigators in the selection of variants for study in vitro or in novel genetic association studies. The Genewindow application and source code will soon become publicly available for use in other genomes, and can be integrated with the analysis, storage, and archiving of data generated in any laboratory setting. This can assist laboratories in the choice and tracking of information related to genetic annotations, including variations and genomic positions.
purpose
  • Intuitive representation of genomic variation using advanced web-based graphics (SVG)
  • Search by HUGO gene symbol, dbSNP ID, internal CGF polymorphism ID, or chromosome coordinates
  • “Gene-centric” display (only when a gene of interest is in view) oriented 5’ to 3’ regardless of the reference strand and adjacent genes
  • Two views, a Locus Overview, which varies in size depending on the gene or genomic region being viewed and, below it, a Sequence View displaying 2000 base pairs within the overview
  • Navigate the genome by clicking along the gene in the Locus Overview to change the Sequence View, expand or contract the genomic interval, or shift the view in the 5’ or 3’ direction (relative to the current gene)
  • Lists of available genomic features
  • Search for sequence matches in the Locus Overview
  • Genomic features are represented by shape, color and opacity with contextual information visible when the user moves over or clicks on a feature
  • Administrators can insert newly-discovered polymorphisms into the Genewindow database by entering annotations directly through the GUI
  • Integration with a Laboratory Information Management System (LIMS) or other databases is possible
Added March 9 2005
  • Users can now filter SNPs by dbsNP submitter (e.g. HapMap SNPs) or by frequency.
 features
  • Population linkage disequilibrium and haplotype tagging SNPs, based on CGF data, will be displayed.
  • Users will be able to download data from the web site based on the gene or genomic interval they are viewing.
 upcoming
Supplemental material provides additional information about Genewindow.
supplement
For questions, comments, and suggestions please write to genewindow@mail.nih.gov. To learn more about the CGF and our bioinformatics please visit the CGF and SNP500Cancer web sites.
contact
The content of this web site does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government.

Genewindow includes data from multiple public resources. As a result, the data presented can sometimes be incorrect or inconsistent. Genewindow does present validated data on polymorphisms from the CGF pipeline when available.

 disclaimer