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Motif search for basic patterns
The Motif Search function searches for defined/known motifs or sequence patterns. Patterns and motifs can be searched with different levels of degeneracy in both DNA and protein sequences, and the analyses can be performed on one or more sequences at a time.
Various parameters can be set prior to the search:
- Motif – i.e. a search string or motif of interest- Ambiguous amino acids and nucleotides are allowed. Example: ATGATGNNATG
- Accuracy of the search string to the match on the sequence.
- Table output. Opens the found motifs or patterns in a table view. It is possible to see one table per sequence but it is also possible with one table for multiple sequences.
- Add motif to sequence as annotation. Check this box to add found search strings as annotations on the sequence.
More information on each found motif or pattern is available through the tooltip option, including detailed information on the position of the pattern and how identical it was to the search string.
Tabular view
The results can also be shown in a tabular view. Such view includes motifs or patterns found, either in one combined table, or in individual tables if multiple sequences were selected.
The table includes each pattern found, their positions in the sequence, and the obtained accuracy score per sequence.
