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Aptean GenomeQuest: Variation Detection Tool

Aptean GenomeQuest: Variation Detection Tool


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Aptean GenomeQuest: Variation Detection Tool

12 Nov 2021


Hi. Today, I'd like to introduce GenomeQuest's new variation module. The variation module allows the searcher to quickly identify position-specific and residue-specific variations across patent sequences. Filters allow searchers to target hits with specified variants or specified fixed residues and a variant report summarizes the variation landscape.

The new GenomeQuest sequence variation module uses algorithms that allow a searcher to capture previously-unknown variants, unlike traditional methods and variant filters can be applied in conjunction with the standard GenomeQuest filters. Creating new filters will be intuitive to GQ searchers. Simply create and name a filter, and select from a menu of options that provide multiple methods to highlight and filter your data.

In this example, I am searching for any and all replacements over the length of my query sequence. This method can be a great starting point to determine overall variation. GenomeQuest filters can be built with both broad or specific variation, specifying multiple residues at a position and/or locking down regions.

In this case, the filter that I have created requires all of these variants to be present. A boolean "and." The GenomeQuest sequence variation discovery module can also create the same variant requirements with the Boolean "or," which will require at least one of the desired variants. Our Landscape Report provides the searcher with a summary view of the data including sequence variation-based highlighting and a global variation table.

The sequence display highlights regions with differing levels of variation with red being highly variable and black being fixed. Here we see our Boolean "or" and our Boolean "and" with much less variation. The variation module also allows the searcher to highlight specific regions without filtering.

Here, we see CDRs highlighted on a variable chain. Each CDR can be configured with differing levels of variation, or simply highlighted. By filtering for any or no replacement, CDRs can be highlighted on a chain without reducing the headcount.

This next filter was created to require a locked CDR-1, broad variation in CDR-2, and a specific residue in CDR-3, highlighting and filtering on on the specific residue while also highlighting the CDR region. This methodology is described on this slide. This concludes today's demonstration of the new GenomeQuest sequence discovery variation module. Thank you.

Discover more about Aptean GenomeQuest and its Variation Detection Tool, a feature of the comprehensive biological IP database from Aptean. Get in touch with our team of experts today to get started.

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