Antibody Annotator sometimes puts this qualifier on V(D)J regions if there is a frameshift very early in the variable region, and the majority of the sequence is in a different frame to the beginning. If the selected annotation has a "codon_start" qualifier then that will be used as the translation frame. By default, it will translate from the beginning (frame 1) of the selected region for each sequence. This operation will translate nucleotide sequences according to the selected genetic code and translation frame before aligning the sequences. Translate Nucleotide Sequence(s) Prior to Alignment If you choose to translate, you will need to specify a translation frame (relative to the start of the sequence). Entire sequence : This operation will align all the selected sequences from the 5' end to the 3' end, disregarding any annotations.Learn more here: Using Feature Databases to identify Fusion Proteins Sequences that don't have that region will be skipped, and won't appear in the resulting alignment.Īny custom regions added via annotation using a feature database can also be selected for alignment. The help text below the selector will show you what order your regions will appear in, and you can see how many sequences contain the region beside the region name. This will concatenate all the selected regions for each sequence, and then show the resulting alignment. Align Regions: To align multiple regions, hold down command (MacOS) or control (PC) and click on the region(s) you would like to align.You can also align across the entire sequence, ignoring any annotations. You can align either a single region, or align multiple regions and/or genes at once. To the right of the Sequence Logo, you can select to plot the amino acids by Frequency or Entropy, and colour the amino acids by a variety of options. You can also view the sequence logo for any alignment by switching to the Sequence Logo tab: Sequences that do not have any of the specified regions will be skipped and won't show in the alignment. If some of your sequences are missing one or more of your selected regions, this will be indicated by a region not found annotation (see below). Skip to this section to learn how to view assay data with your alignment. ***Note that the above alignment has Assay Data values attached. The example below with both the Heavy and Light CDR3 was created using the associated Heavy/Light chains from the Sanger Tutorial 2 data. When scFv sequences or associated Heavy/Light chain pairs are aligned, the resulting alignment will contain the relevant sections of each chain, concatenated in the same row. You will never get a residue from CDR1 aligning in the same position as a residue from CDR2. In the example below, this means that all the Heavy CDR1s will align together, all the CDR2s will align together, and so on. If you select multiple regions, these will always align internally. Jump to this section to learn more: Viewing Assay Data in your Alignments. If you have added Assay Data to your sequences prior to alignment, these values can be represented alongside your alignment. To align sequences from a Biologics Annotator Result document, (1) select a Biologics Annotator Result document, (2) select two or more sequences in the All Sequences table and click Post-processing > Align in the dropdown. The other videos in our Getting Started series may also be helpful, linked here. A brief video tutorial is embedded below. This article outlines how to perform a Sequence Alignment in Geneious Biologics. Aligning sequences is a good way of visually comparing sequences, and can include a tree, assay data, and cluster information.
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