Overview: Development of softwareanalysis tools for:

1
Nickerson PGA - SeattleSNPs - Bioinformatics
Component
Overview Development of software/analysis tools
for 1) Processing of data from
sequencing-based SNP discovery projects a)
Laboratory data flow tracking b) Automated
processing/statistics c) Streamlining of data
submission to national database resources d)
Development of web site for rapid dissemination
of SNP data 2) Visualization of SNP data
following processing a) Integrated views of data
with other genomic information b) Automated
viewing of haplotype/phylogenetic data
(tree-building) 3) Analysis of SNP data for
a) Descriptive statistics b) Haplotype
estimation from SNP data b) Linkage
disequilibrium against expectations from
coalescent simulations
2
Nickerson PGA - SeattleSNPs - Bioinformatics
Component
Resources currently under development 1)
Develop software tools for automation of SNP
discovery and analysis a) PCR-Overlap (PCR
primer picking - perl). b) Improvement of
software for automation of SNP discovery
from sequence-based data (Polyphred -
C). c) Visualization tools for analysis of
SNP data (perl). d) Software used for
integration with other high-throughput
sequence analysis software (i.e. Phred,
Phrap). e) Post-processing of SNP data -
descriptive statistics/database submission
(perl). f) Software for coalescent simulations,
haplotype inference, generation of
phylogenetic trees, and analysis of linkage
disequilibrium (SNP vs SNP correlations)
(perl/C). g) Algorithms for SNP site
selection for genotyping(C) 2) Develop highly
integrated LIMS - Oracle database for
tracking laboratory work flow and SNP discovery
results (generalized for other laboratories)
(PL/SQL, Java/Javascript, Web interface).
3
Nickerson PGA - SeattleSNPs - Bioinformatics
Component
Current Status and Future Directions Highlights
1) Web site for distribution of SNP data
implemented. Data being posted since
January. 2) Completion of initial LIMS Oracle
database design. Testing of database schema and
integration into laboratory work
flow. Development of Web-based interface for
database for data distribution -- planned to be
available in next 6 months to allow customized
data queries. 3) Completion of scripts for
automated processing of SNP data following
sequencing based discovery. Data posted
automatically to web site. Semi-automated submis
sion to national databases. 4) Improvements
being made to SNP discovery software
(PolyPhred). 5) Automation of coalescent
simulations and linkage disequilibrium
analysis. Distribution of this software planned.