Welcome to SubSeqer

SubSeqer is a webtool aimed at uncovering meaningful sequence motifs in low complexity protein sequences. It uses a novel subsequence visualization method to build motifs by identifying relationships between small subsequences within the larger sequence. SubSeqer differs from traditional sequence motif finding tools through the application of a unique graph based approach similar to that employed to visualise protein-protein interaction networks. In graphs generated by SubSeqer, nodes represent subsequences while edges represent connections between adjacent subsequences. This approach enables the identification of key "hub" (i.e. highly connected) subsequences that likely mediate important structural and/or functional roles within a variety of different sequence contexts. Further details of its operation and examples of its application are provided in the Overview and Applications sections respectively.

SubSeqer is simple to use, and can be completed in four steps illustrated in the graphic below: sequence submission; preliminary analysis and parameter refinement; network visualizaion; and motif extension using sequence logos. For more information on how to use SubSeqer, please see the Documentation page.

Step 1: Sequence Insertion and Parameter Selection

Sequence (in FASTA format):

NB. While SubSeqer is a robust tool for low complexity sequences such as elastin, collagen, and spider silks, it may not be suitable for all protein sequences. If SubSeqer determines that the submitted sequence has too many overrepresented nodes, it will warn you of the situation and will not display the subsequence interaction graph.
Let SubSeqer help me determine parameters (recommended)

SubSeqer will show you the subsequence distribution of your sequence using a number of common subsequence lengths and wild card numbers. From these distribution graphs, you can select the parameters most suitable for your submitted sequence. This method is recommended for most users. (Help)

Let me input my own parameters

If you know exactly what subsequence size and wild card numbers you want, please choose this option and enter the values below. (Help)

Subsequence size:
Number of wildcards:
Percentile Odds Score Cutoff: