Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS)


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


Software Information
Java VersionPrimeFaces VersionTomcat VersionDatabase Version
Java 8 Enterprise Edition ( PrimeFaces 11.0 ( Tomcat 8.5 ( 10.3.39

NCBI Information (See References)
Data VersionInstallation DateSeqAPASS VersionBLAST+ VersionProtein and Taxonomy DatabaseCDD DatabaseCobalt DatabaseCobalt VersionI-TASSER VersionTM-align VersionUniProt Database
801/26/2024 03:00 PM7.12.15.001/11/202309/21/202208/03/20230.755.22021022401/19/2024
709/05/2023 04:00 PM7.02.13.004/25/202202/23/202107/09/20100.755.22021022408/01/2023
706/07/2022 01:00 PM6.12.13.004/25/202202/23/202107/09/20100.75--
609/14/2021 01:00 PM6.02.11.004/28/202102/23/202107/09/20100.75--
607/15/2021 04:00 PM5.12.11.004/28/202102/23/202107/09/20100.75--
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. 14, 2023


NCBI Protein Database
Pruitt, K. D., Tatusova, T., Maglott, D. R. (2007). NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic acids research, 35(suppl_1), D61-D65.

NCBI Taxonomy Database
Federhen, S. (2012). The NCBI taxonomy database. Nucleic acids research, 40(D1), D136-D143.

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., Lipman, D. J. (1990). Basic local alignment search tool. Journal of molecular biology, 215(3), 403-410.

NCBI Conserved Domain Database
Marchler-Bauer, A., Zheng, C., Chitsaz, F., Derbyshire, M. K., Geer, L. Y., Geer, R. C., ... & Bryant, S. H. (2012). CDD: conserved domains and protein three-dimensional structure. Nucleic acids research, 41(D1), D348-D352.

Papadopoulos, J. S., Agarwala, R. (2007). COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics, 23(9), 1073-1079.

ECOS Environmental Conservation Online System
US Fish and Wildlife Service. (2018). ECOS Environmental Conservation Online System. Website[accessed 26 June 2023].

ECOTOX Knowledgebase
Olker, J.H., Elonen, C.M., Pilli, A., Anderson, A., Kinziger, B., Erickson, S., Skopinski, M., Pomplun, A., LaLone, C.A., Russom, C.L., Hoff, D. (2022). The ECOTOXicology knowledgebase: A curated database of ecologically relevant toxicity tests to support environmental research and risk assessment. Environmental Toxicology and Chemistry, 41(6), 1520-1539.

CompTox Chemicals Dashboard
Williams, A.J., Grulke, C.M., Edwards, J., McEachran, A.D., Mansouri, K., Baker, N.C., Patlewicz, G., Shah, I., Wambaugh, J.F., Judson, R.S., Richard, A.M. (2017). The CompTox Chemistry Dashboard: a community data resource for environmental chemistry. Journal of cheminformatics, 9, 1-27.

Rose, P.W., Prlić, A., Altunkaya, A., Bi, C., Bradley, A.R., Christie, C.H., Costanzo, L.D., Duarte, J.M., Dutta, S., Feng, Z., Green, R.K. (2016). The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic acids research, gkw1000.

Yang, J., Zhang, Y. (2015). I-TASSER server: new development for protein structure and function predictions. Nucleic acids research, 43(W1), W174-W181.

Varadi, M., Anyango, S., Deshpande, M., Nair, S., Natassia, C., Yordanova, G., Yuan, D., Stroe, O., Wood, G., Laydon, A. and Žídek, A. (2022). AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic acids research, 50(D1), D439-D444.

Zhang, Y., Skolnick, J. (2005). TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic acids research, 33(7), 2302-2309.

SeqAPASS Help:
For SeqAPASS user guide and data visualization workspace, click here.