A Typical Display for SNPCEQer II
 
  
 
 
 
 
Identify SNPs in DNA Sequences
 
 
DNA sequences should be in .phd format. To display chromatograms for the DNA sequences, the corresponding trace files in the scf format should be in the same folder
  
 
 
 
 
Open the SNP Report File
 
 
 
The SNP report file is named as SNP.snp that is stored in the sequence data folder
 
 
  
 
 
 
 
 
 
The SNP report file is displayed in the first pane after it is opened
 
 
  
 
 
 
 
 
Double clicking on the position line of the SNP will display the corresponding chromatogram in the second pane
 
 
  
 
 
 
 
Placing the cursor on the position line of a SNP, pressing the shift and space keys simultaneously will display the chromatogram of this sequence in the third pane for comparison.
 
 
 
 
 
 
 
Using mouse left button to define the region of the chromatogram to be magnified, when the button is released, the chromatogram is magnified. Pressing  ‘z’, the original chromatogram will be displayed.
 
 
 
 
 
 
 
Double clicking in the chromatogram pane, a window will be popped up so that the chromatogram can be customized and the data can be exported.
 
  
 
 
 
Determine SNP Mutation Type
 
Placing the cursor on the position line of a SNP and selecting the “Mutation_Type” in the Analysis menu, a pop-up window will show up with the consensus sequence and position of the selected SNP displayed. The user type in the position of a codon upstream of the selected SNP, the program will report if the SNP cause a synonymous mutation or non-synonymous mutation.
 
 
 
 
 
 
Search NCBI Databases
 
Placing the cursor on the position line of a SNP and selecting the searching method such as “Blast_dbSNP” in the database menu, a pop-up window will display the selected sequence.  The user can edit the sequence in the edit box.  After press “OK” button, the sequence will be blasted against dbSNP automatically.  Follow the same procedure to search NCBI DNA and protein databases.
 
  
 
 
 
SNP Submission to dbSNP
 
   
Placing the cursor on the position line of a SNP and selecting the “Submit_to_dbSNP” in the database menu, a submission file (called “submission.txt”) will be generated in the data folder for submission. The user must fill in the required data fields in the submission file before it is submitted.