SNP : impact structure - function DB

SNP : impact structure - function DB

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

Results integrated in web interface

Location image

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

GALT-DB server


  1. Glucokinase and Tyrosine Phosphatase ^
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WPdrx
Physiologist Bioinformatician
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