We’re reading and incorporating your feedback! As requested, you can now search for sequences in our Multiple Sequence Alignment (MSA) Viewer. You can search the anchor or consensus sequence of a multiple alignment for short sequence strings. This new feature allows you to:
- Look for a sequence motif in DNA or protein alignments in order to confirm the presence of a probe or PCR primer.
- Check whether your sequence has matches in multiple locations on the anchor or consensus.
- Examine the sequence similarity within the alignment of your match.
Look for the new “Find” button on the MSA toolbar (Figure 1).
Figure 1: “Find” button on MSA toolbar
Use this button to search for a nucleic acid sequence on nucleic acid alignments, or an amino acid sequence on protein alignments. Standard IUPAC terminology is recognized, including ambiguous nucleotide symbols like R and Y.
A pop-up window displays the search results (Figure 2). If you’re viewing a nucleic acid alignment, MSA will search the consensus or anchor sequence in both orientations, and report the orientation of the match.
Figure 2: Window display of search results for “tagty” sequence
Double click on the search result to go directly to that location in the anchor or consensus row of the alignment.