SeqAPASS Version 4.0 Adds New Interactive Help Menus and Interoperability with Other Online EPA Tools
Published November 4, 2019
There are limited amounts of toxicity data on many chemicals in commerce, and much of what is available does not describe potential adverse effects across different species. To help close this gap, EPA scientists have recently released version 4.0 of the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool.
SeqAPASS is a publicly available online tool that uses protein sequences to help understand how chemicals will affect different species. To make these predictions, SeqAPASS starts by looking at what proteins a chemical interacts with to produce a toxic effect. It then looks to see if those same protein sequences are present in other species to determine whether a chemical might produce a similar effect in another species.
The new version of SeqAPASS includes interactive help menus and guidance for setting up appropriate protein comparisons. The new version also adds interoperability with other EPA tools, like the ECOTOX Knowledgebase.
The new help features were added in response to feedback from SeqAPASS users who wanted greater guidance for identifying SeqAPASS query proteins and information on critical amino acid residues. Users also requested information buttons throughout the tool describing features with summary tables to more rapidly interpret the results of SeqAPASS. User feedback is a critical part of helping SeqAPASS evolve and all the new features added in version 4.0 were in response to user requests.
Version 4.0 is also the first version that includes interoperability with the ECOTOX Knowledgebase, linking the protein-based predictions of chemical susceptibility from SeqAPASS to the empirical toxicity data found in ECOTOX. It works by linking to the ECOTOX Explore by Species option, where the user can view all toxicity data curated for that species in the ECOTOX Knowledgebase. From there, the user can select their chemical of interest to view whether there is empirical evidence to suggest the chemical causes an adverse effect for the corresponding species in SeqAPASS.
SeqAPASS has been applied to key EPA projects including understanding potential chemical susceptibility to endangered or threatened species, identification of the species most likely to be susceptible to a chemical, and for initial considerations in extrapolating high-throughput screening data from mammalian-based assays to other vertebrates.
With the new features available in version 4.0, SeqAPASS will continue to be a valuable tool for both researchers and risk assessors who are interested in understanding how different species may be affected by chemical exposure.
