The SeqAPASS Tool was developed by Dr. Carlie LaLone and the
Environmental Modeling and Visualization Laboratory for:
U.S. Environmental Protection Agency,
Center for Computational Toxicology and Exposure
Great Lakes Toxicology and Ecology Division,
Duluth, MN
Contact:
SeqAPASS.support@epa.gov
Threatened/Endangered Species Data obtained from EPA ECOTOX on Feb. 2, 2022
References:
SeqAPASS Method
LaLone, C. A., Villeneuve, D. L., Doering, J. A., Blackwell, B. R., Transue,
T. R., Simmons, C. W., Swintek, J. A., Degitz, S. J., Williams, A. J., Ankley,
G. T. Defining the Taxonomic Domain of Applicability for Mammalian-Based
High-Throughput Screening Assays. Environmental Science and Technology. 2018 Oct;
52(23), 13960-13971. [PubMed PMID: 30351027] https://pubs.acs.org/doi/10.1021/acs.est.8b04587
https://pubs.acs.org/doi/10.1021/acs.est.8b04587
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Doering, J. A., Lee, S., Kristiansen, K., Evenseth, L., Barron, M., Sylte, I.,
and LaLone, C. A. In silico site-directed mutagenesis informs species-specific predictions
of chemical susceptibility derived from the Sequence Alignment to Predict Across Species
Susceptibility (SeqAPASS) tool. Toxicological Sciences 2018 July; 166(1), 131-145. [PubMed
PMID: 30060110] https://academic.oup.com/toxsci/article/166/1/131/5060571
https://academic.oup.com/toxsci/article/166/1/131/5060571
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LaLone, C. A., Villeneuve, D. L., Lyons, D., Helgen, H. W., Robinson,
S. L., Swintek, J. A., Saari, T.W, Ankley, G. T. Sequence Alignment to Predict
Across Species Susceptibility (SeqAPASS): A web-based tool for addressing the
challenges of cross-species extrapolation of chemical toxicity. Toxicological Sciences
2016 Oct; 153(2): 228-245. [PubMed PMID: 27370413]
https://academic.oup.com/toxsci/article/153/2/228/2578709/Editor-s-Highlight-Sequence-Alignment-to-Predict
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LaLone, C. A., Villeneuve, D. L., Burgoon, L. D., Russom, C.
L., Helgen, H. W., Berninger, J. P., Tietge, J. E., Severson, M. N.,
Cavallin, J. E., Ankley, G. T. Molecular Target Sequence Similarity as
a Basis for Species Extrapolation to Assess the Ecological Risk of
Chemicals with Known Modes of Action. Aquatic Toxicology 2013 Nov;
144-145:141-154. [PubMed PMID: 24177217]
http://www.sciencedirect.com/science/article/pii/S0166445X13002312
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NCBI Protein Database
Pruitt, K. D., Tatusova, T., Maglott, D. R. NCBI reference
sequences (RefSeq): a curated non-redundant sequence database of
genomes, transcripts and proteins. Nucleic Acids Research 2007 Jan;
35:D61-65. [PubMed PMID: 17130148]
NCBI Taxonomy Database
Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H.,
Canese, K., Chetvernin, V., Church, D. M., DiCuccio, M., Edgar, R.,
Federhen, S., Geer, L. Y., Kapustin, Y., Khovayko, O., Landsman, D.,
Lipman, D. J., Madden, T.L. , Maglott, D. R., Ostell, J., Miller, V.,
Pruitt, K. D., Schuler, G. D., Sequeira, E., Sherry, S. T., Sirotkin,
K., Souvorov, A., Starchenko, G., Tatusov, R. L., Tatusova, T. A.,
Wagner, L., Yaschenko, E. 2007 Jan; 35:D5-12. [PubMed PMID: 17170002]
NCBI BLAST
Altschul S. F., Gish, W., Miller, W., Myers, E. W., Lipman, D.
J. Basic local alignment search tool. Journal of Molecular Biology 1990
Oct 5; 215(3):403-10. [PubMed PMID: 2231712]
NCBI Conserved Domain Database
Marchler-Bauer, A., Zheng, C., Chitsaz, F., Derbyshire, M. K.,
Geer, L. Y., Geer, R. C., Gonzales, N. R., Gwadz, M., Hurwitz, D.I.,
Lanczycki, C. J., Lu, F., Lu, S., Marchler, G.H., Song, J.S., Thanki,
N., Yamashita, R. A., Zhang, D., Bryant, S.H. CDD: conserved domains
and protein three-dimensional structure. Nucleic Acids Res. 2013 Jan
1;41(D1):D348-52. Epub 2012 Nov 28. [PubMed PMID: 23197659]
Marchler-Bauer, A., Bryant, S. H. CD-Search: protein domain
annotations on the fly. Nucleic Acids Res. 2004 Jul 1;32(Web Server
issue):W327-31. [PubMed PMID: 15215404]
NCBI COBALT
Papadopoulos, J. S., Agarwala, R. COBALT: constraint-based
alignment tool for multiple protein sequences. Bioinformatics 2007 Mar 1;
23:1073-79. [PubMed PMID: 17332019]
SeqAPASS Help:
For SeqAPASS user guide and data visualization workspace,
click
here.
