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.
Missed a few videos on YouTube? Here’s the latest from our channel.
Customize the MSA Viewer to Make Your Analysis Easier
We’re constantly improving the Multiple Sequence Alignment (MSA) Viewer. This video demonstrates several new and popular features, including the ability to change data columns, hide selected rows, analyze polymorphisms, and more.
We’re excited to report that researchers using the NCBI Multiple Sequence Alignment Viewer (MSAV) can now add or remove columns from the alignment view. In this way, you can choose to show only columns with data relevant for analysis of the sequences in your alignment.
When you arrive at an MSA alignment view, you’ll see columns for the Sequence ID (e.g., sequence accession number), Start and End of the alignment, and the organism (species name).
Sometimes, the information in these default columns isn’t the most useful information for sorting through the alignment. In the example above, all the sequences are from the same organism, so looking at the Organism column won’t help in figuring out the differences among the different sequences in the alignment.
Do you ever wish there was a quick way to hide partial or poor quality sequences from a multiple alignment view? NCBI’s Multiple Sequence Alignment Viewer (MSAV) now allows you to do just that with an easy hide/show rows feature! Hidden rows won’t be shown in the PDF/SVG download, and these sequences will not be included in the FASTA alignment download file.
You can easily manage which rows are shown through the menu available by right-clicking on a row or through the Rows dialog (Figure 1).
Figure 1. The MSA viewer showing the options for hiding or showing rows. Right clicking any sequence row provides options for hiding single or selected rows or restoring hidden rows. You can also manage rows through the edit row dialog activated by clicking the “Rows” button next to the gear icon at the upper-right. Check or uncheck sequences to add or remove them from the display. The “Rows shown” status message at the lower-right of the MSAV indicates the total number of rows in the sequence alignment and the number displayed.
Keep in mind that hiding rows does not re-calculate the alignment, so it’s important to know if any rows have been hidden from your current view. The “Rows shown” message at the lower-right indicates whether you are displaying all rows.
You can find more tips on using the MSA Viewer, including information about anchors, consensus, and coloring settings in our user guide. Please get in touch if you have any questions or suggestions using the Feedback link on the page or writing to the NCBI Help Desk.
Version 3.4.1 of Genome Workbench, NCBI’s sequence annotation and analysis platform, includes new features for the Multiple Sequence Alignment View, the Graphical Sequence View and the Sequence Editing and Submission Package as well as a number of other improvements and bug fixes.
In the Multiple Sequence Alignment View, you can now export publication quality graphics (Save As PDF/SVG … , Figure 1). In the Graphical Sequence View you can now search by locus tag, use improved search capabilities for genes by locus and can better display the selected location in the feature editing dialog when annotating a sequence.
Figure 1. A multiple alignment view in Genome Workbench highlighting the new ability to save presentation quality image files (Save As PDF and SVG formats).
In the Sequence Editing and Submission Package, we rearranged the controls in the Table Reader dialog to fit onto smaller screens and improved importing feature tables that contain mat-peptides (mature peptide) features.
Bug Fixes and Improvements
We have made a number of other fixes and improvements. For MacOS users we fixed blurry text in some dialogs, fixed the copy to clipboard problem, and improved support for the latest Catalina version. We also fixed a crashing problem in the Active Object Inspector interface. You should also see improvements in loading SNP data and better recovery in cases of power outages or other events causing local file corruption.
In the Sequence Editing and Submission Package, we fixed a bug that occurred when applying miscellaneous descriptors and structured comment fields using the Table Reader and an issue with using a PubMed ID to look up a publication.
Please see the extensive help documentation including FAQs, videos, and tutorials linked to the Genome Workbench homepage for more information and examples on how to use Genome Workbench in your research.
You can now download a publication-quality graphic images of the alignment displayed in the NCBI Multiple Sequence Alignment Viewer (Figure 1). Load sequence alignments into the viewer from BLAST or COBALT results or upload alignment files directly. Once you have the the alignment set in the viewer, choose the “Printer-friendly PDF/SVG” option in the Download menu on the toolbar to save the image. The PDF and SVG files contain vector graphics suitable for presentation and publication. Figure 1. The image download options in the MSAV. You can adjust the desired coordinate range and choose to download a PDF or SVG image. You can also preview the PDF download . Choose simplified color shading to improve compatibility with some graphics programs.
The downloaded image will show the coordinate range you requested and will include all the rows in the alignment.
Please contact us through the Feedback link on the MSA Viewer or write to the NCBI Help Desk to provide feedback and let us know how we can make the NCBI Multiple Sequence Viewer work better for you.
The NCBI Multiple Sequence Alignment Viewer (MSAV) is a versatile web application that helps you visualize and interpret MSAs for both nucleotide and amino acid sequences. You can display alignment data from many sources, and the viewer is easily embedded into your own web pages with customizable options. An even simpler way to use MSAV is to use our page, upload your data, and share the link to a fully functional viewer displaying your results.