Note: Please be assured that the information here would be held confidential and
would not be distributed.
Arizona State University
University of Maryland
University of Florida
If you belong to any
organization not mentioned above,
please specify below:
Database(s) used in this pipeline:
(Press and hold 'CTRL' for multiple selections)
Gene Ontology (GO)
Protein Data Bank
If you use any database not mentioned above,
please specify below: Example:
NCBI Cancer Chromosomes,
SNP Gene Viewer, etc.
Application(s) used in this pipeline: Example:
Motivation behind the pipeline:
(Task which is resolved with the pipeline)
Selection of the SNPs previously defined by linkage or association studies
Problem(s) faced in the pipeline:
(Problems faced in accessing the databases/resources)
Takes too long to retreive answers to queries
How do you access/ query the database and what
inputs do you use while querying?:
PubMed is queried with a GENE-ID
you use to solve the task mentioned in motivation.)
a. Reference sequence of the region of interest = input 1
b. Linkage region (initial starting range based on the genetic markers) = input 2
2. Collect SNPs from dbSNP, HGVbase, and Celera that correspond to the base range.
3. Validation: Checks whether the sequences are found in all 3 sources, in 2 or only one (no action is taken).
4. Use the tool MAGMA [HZS+] to select a set of SNPs to maximize the complete and even coverage of the region of interest with as many validated SNPs as possible.
Thank you for your time!