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 Dec. 14, 2023
References:
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. https://doi.org/10.1093/nar/gkl842
NCBI Taxonomy Database
Federhen, S. (2012). The NCBI taxonomy database. Nucleic acids research, 40(D1), D136-D143. https://doi.org/10.1093/nar/gkr1178
NCBI BLAST
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. https://doi.org/10.1016/S0022-2836(05)80360-2
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. https://doi.org/10.1093/nar/gks1243
NCBI COBALT
Papadopoulos, J. S., Agarwala, R. (2007). COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics, 23(9), 1073-1079. https://doi.org/10.1093/bioinformatics/btm076
ECOS Environmental Conservation Online System
US Fish and Wildlife Service. (2018). ECOS Environmental Conservation Online System. Website https://ecos.fws.gov/ecp/[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. https://doi.org/10.1002/etc.5324
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. https://doi.org/10.1186/s13321-017-0247-6
RCSB PDB
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. https://doi.org/10.1093/nar/gkw1000
I-TASSER
Yang, J., Zhang, Y. (2015). I-TASSER server: new development for protein structure and function predictions. Nucleic acids research, 43(W1), W174-W181. https://doi.org/10.1093/nar/gkv342
AlphaFold
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. https://doi.org/10.1093/nar/gkab1061
TM-align
Zhang, Y., Skolnick, J. (2005). TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic acids research, 33(7), 2302-2309. https://doi.org/10.1093/nar/gki524
SeqAPASS Help:
For SeqAPASS user guide and data visualization workspace,
click
here.
