A graphic tool to visualize DNA sequences...







SequenceViewer includes the DNAViewer and RepeatsViewer tools.  These windows based computer programs creates graphical images from text DNA sequences in FASTA format. The images created by the tool can help in identifying repeating patterns, letter concentrations in different regions and possibly give clues about the DNA physical structure.


How do they work?

DNAViewer is working on a sequence file and generates images based on the start index specified, letter orientation and colors. The image is a line that changes direction and color based on the next letter in a sequence. RepeatsViewer works on two files, one is the row sequence and the second file is a text file with lines containing a start index, an end index and a consensus size. The program generates images of the patterns specified in the second file. The program can be used to view other found patterns i.e. transcription factors or Z-DNA candidates.


Getting started…


Download the program using the link from this page. Double click on the setup file and install the application. DNAViewer requires you to specify an input file in FASTA format. RepeatsViewer will prompt you with a setup dialog where you have to specify the sequence file and found repeats file. You can download the C.Elegans sequence and found repeats files from this site as a sample to get you started.


Screen Shots













Found Repeats in C.Elegans Chromosome1


Find repeats using the Tandem Repeat Finder program

Find repeats and create a text files using the tools->data download link from the  Tandem Repeats Database

Download and view more sequences from NCBI

Image Gallery

Tandem Repeats of consensus size 43 found in C. Elegans Chromosome 1 in As cancels Ts and Cs cancels Gs Orientation

The beginning of C. Elegans Chromosome 1 in the three possible letter orientations


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