New feature in the MSA viewer: Search for a short sequence

New feature in the MSA viewer: Search for a short sequence

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.

Please refer to our user guide for more tips on using the MSA Viewer. Send us feedback or contact the NCBI Help Desk if you have any questions or suggestions.

Leave a Reply