Mellau Consulting

Mutation analyis

The SequenceViewer program and the use of DNAMatch with sequence data is only in an experimental status (version 1.0.3. ). Using the SequenceViewer in combination with DNAMatch you may be able to execute human identification using DNA sequences or detect mutations in DNA Sequences

Also you may use DNAMatch for screening larger sets of sequence files for mutations in the DNA sequence. In the following  two possible uses of DNAMatch in sequence analysis are shown using the Demo1 CE data file.

 

METHOD 1. Using the Fragment control system

 

This method works if

  • You want to check if a given sequence is present or not in the selected CE data file. You can detect possible mutations or use DNAMatch for human identification through SNP analysis (or any other sequence based technique).
  • You created your own MarkerList/MarkerDatabase file with the sequence(s) that you want to check in the files to be analysed.

    • Source of CE data files

    The following steps MUST be followed exactly for a correct DNA Sequence analysis :

  • Start Symath
  • Click  button.
  • Load the CE file clicking the  on the SequenceViewer WorkSheet.
  • Click the  button.

    • DNAMatch set up for sequence analysis

     Just after the start, DNAMatch is not ready for this type of analysis. First you have to switch the   button to  and load the ABI377SequenceDatabaseDemo1.mdb file (created using the List type database SequenceViewerDemo1.nb) as shown on the next figure :

    Now you have to click the “STR Kit” button to move the Sequence data from the selected MarkerDatabase in the File data and set the sample type parameter to “allelic ladder” as shown on the left figure.

    Also you have to switch the option buttons to  and   .

    Starting the analysis

    Click on the  button to execute the sequence analysis and on the   button to display the analysis results.

    Analysis results if no mutations are present

    The following figures show the tables and plots drawn in case of a perfect match. The meaning  of x-es and colours is the same as in the fragment analysis. The assignment to A, T, C, G is done by DNAMatch, the initial sequence imported from the ABI file is ignored.

    Analysis results if  mutations are present 

    The following figures show the tables and plots drawn in case of a detected mismatch. In the sequence table a red symbol is displayed if a mismatch was detected (the peak was expected in the A trace only but actually it was detected  in the C trace). The labelling on the plot for mismatch peaks is done using the expected label (here A). Which sequences to use for check, which differences to allow and which  should be reported are user defined in the MarkerDatabase. In principle the system can be set up for any practical sequence analysis task. If you are interested in using DNAMatch in sequence analysis as described in this section please contact info@mellau.de.

    What you have to do after the analysis is terminated

  • Inspect the plots and tables.
  • Print the analysis results
  • CLOSE Symath and redo the steps for another data file
    		•

    METHOD 1. Using the Fragment analysis system

     

    This method works if

  • For any CE sequence file up to 600 bp

    • Source of CE data files

    Import the CE data file as explained in method 1.

    DNAMatch set up for sequence analysis

    The steps to do are the same as in method 1 with the difference that the MarkerDatabase to load is the file ABI377SequenceAnalysis.mdb (created using the List type database ABI377SequenceAnalysis.nb).

    A FragmentJob sample type (as the default  “sample”) has also to be selected.

    Starting the sequence analysis

    Click on the  button to execute the sequence analysis and onthe  “Show” button to display the fragment analysis results.

    Displaying the analysis results

    The sequence analysis results are shown on the sequence tables and plots. You may increase the size of the plots.