Context
SNPs are among most represented mutations and responsible of a wide implication of phenotype variation, particularly due to structural alterations. Lot of data that may infer structural SNPs impact is available online but remains scattered and flawed.
Aims
- aggregate available data;
- generate missing data;
- attribute predictive structure impact values;
- provide data-sets as input to an associated visualization project;
- automatize most of the pipeline.
Method
Collect genomics and protein data
quality control, consistency and standardization
indicator generation for structural study (protocol GALT-DB)
Technically speaking
- Scripting : Perl / Python / Bash
- Data formats : FASTA / PDB / CSV / HTML / JSON /
- Data gathering : SQL / API / Parsing / MySQL Workbench
Software and online web-services
- MODELLER Software, DSSP Software, NACCESS, HBPLUS, Ligplot, Salt Bridge detection script
- Web-services : Consurf web-service, Dezyme PopMusic web-service
Results integrated in web interface
Results status (based on 2 enzymes1)
| Component | Result |
|---|---|
| quality | consistent with published data |
| automation | partial |
| effects | structural destabilization |
Coming features
Associated publications
Master Thesis : Variants DB
Related link
GALT-DB server
- Glucokinase and Tyrosine Phosphatase ^
