Motif Searching

You may sometimes want to identify sequences that contain specific, functionally important patterns, which might influence binding activity or other key properties. In some cases, you may only care about finding sequences that contain an exact region of interest and are less concerned about the rest of the sequence. In other scenarios, you might want to find sequences similar to yours but with certain positions allowed to vary among a set of residues, such as those with similar chemical properties, for example, negatively charged amino acids.

In both situations, Motif Search is ideal. It lets you define exactly where variation is allowed and use degenerate codes to represent multiple possible amino acids at specific positions. This gives you precise control over which residues can mutate while still capturing all sequences that match your motif.

Overall, Motif Search is more targeted than a standard sequence search. Instead of comparing full-sequence similarity, it focuses on matching the key regions that matter most to your analysis.

When performing a motif search, enter your sequence code into the query box. The query box supports the input of degenerate characters.

After entering your sequence, on the right side of the screen, apply the appropriate filters of interest. 

The results page will display sequence codes that pertain to the search query. Select the "Patent" tab to look at related patent results:

You can opt to view the patents on the analytics platform by clicking the "View in Analytics" button. Viewing patents on the Analytics platform allows you to easily save the patents into a workspace and navigate through the patents using the tools available in the workspace.

Motif Search use cases:

• Matching to sequence variants (Single nucleotide polymorphisms, alleles, CRISPR variants)
• Searching for the degenerate sequence: a type of Sequence Markush (a number of sequences in patents have residues such as XXXX or NNN)
• Searching for protein domains or sequence patterns (drug discovery)