Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS)

About


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

Software Information
Java VersionPrimeFaces VersionTomcat VersionDatabase Version
Java 8 Enterprise Edition (http://www.oracle.com/technetwork/java/javaee)Java PrimeFaces 7.0 (http://primefaces.org)Apache Tomcat 8.5 (https://tomcat.apache.org/)MariaDB 10.3.30

NCBI Information (See References)
Data VersionInstallation DateSeqAPASS VersionBLAST+ VersionProtein and Taxonomy DatabaseCDD DatabaseCobalt DatabaseCobalt Version
607/15/2021 04:00 PM5.12.11.004/28/202104/29/202007/09/20100.75
512/01/2020 04:30 PM5.02.10.006/08/202004/30/202007/09/20100.75
508/25/2020 12:00 PM4.12.10.006/08/202004/30/202007/09/20100.75
410/24/2019 10:30 AM4.02.8.102/28/201912/08/201607/09/20100.75
405/15/2019 10:45 AM3.22.8.102/28/201912/08/201607/09/20100.75
303/04/2019 05:54 PM3.12.6.010/25/201712/08/201607/09/20100.75
303/10/2018 02:12 AM3.02.6.010/25/201712/08/201607/09/20100.75
205/24/2017 06:59 PM2.02.5.001/04/201702/05/201607/09/20100.75
101/27/2016 08:00 PM1.02.3.011/09/201604/25/201507/09/20100.75

Threatened/Endangered Species Data obtained from EPA ECOTOX on Dec. 1, 2020



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 Exit

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 Exit

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 Exit

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 Exit

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 below:
SeqAPASS user guideExit
Data visualization (Must download R: https://www.r-project.org/Exit) RDataExit
Data visualization User guide pdfExit