SNPs Mapping System

To any user-specified protein the Functionally Annotated Japanese Protein Structural Information (FUJI) database expeditiously identifies various relevant data including structural information and displays them. SNPs Mapping System is the extension of FUJI database and display the distribution of SNPs on 3D structure.

This work was supported by the Targeted Proteins Research Program (TPRP) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan.

[Use the FUJI database]

How to use

Step1.Input the nucleotide sequence or a gene symbol.

Step1 To find the target gene, input a gene symborl. Database searching was used for gene symbol. If there are multi target gene found based on inputed gene symbol, a list was shown, and user select one to go to Linear Display.





Step1 To find the target gene, input a nucleotide sequence in one letter symbols which may contains SNPs. BLAST searching was used for nucleotide SNP sequence, during which the HIT with highest score was chosen, and the different parts were determined as user defined SNPs.

Step2.Linear Display of the target gene protein structure.

Step2 Alignments to PDB and SCOP structures are displayed linearly, with the N-terminus shown at the left. The dbSNP and user defined SNPs for this gene are also positioned and displayed linearly. In the same screen are shown Pfam and SMART domain alignments, the most conserved region, predicted disordered, SEG, and coiled-coil regions, the prediction of a signal sequence, trans-membrane domains, subcellular localization, and function..

Step3.Three dimensional display of the protein.

Step3 If structural alignments exist, the positioned dbSNP and user defined SNPs are displayed three dimensionally.

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