PAAS: Fast Retrieval of Plant Amino Acid Substitutions and Their Effects on Comparative Phenomics
Tóm tắt
PAAS (Plant Amino Acid Substitutions) is a web database that provides a comprehensive collection of single amino acid substitutions and plant phenotype effects. It gives direct access to the query for comparative phenotype among different species. From here, users can obtain detailed annotation of each variants, substitution combination, and corresponding protein effects. Currently, PAAS covers 4,749 manually curated single amino acid substitutions scattered throughout 1,313 proteins from 111 plant species. PAAS should be an efficient resource for researchers to facilitate gene function understanding, produce rationally designed protein, as well as improve plant desirable traits. The database is implemented in PHP MySQL JavaScript and can be accessed at
http://paas.fruitech.org/
without registration.
Tài liệu tham khảo
Cooper L, Walls RL, Elser J, Gandolfo MA, Stevenson DW et al (2013) The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol 54:e1
Henikoff S, Comai L (2003) Single-nucleotide mutations for plant functional genomics. Annu Rev Plant Biol 54:375–401
Jia G, Huang X, Zhi H, Zhao Y, Zhao Q et al (2013) A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet 45:957–961
Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009) The SWISS-MODEL repository and associated resources. Nucleic Acids Res 37:D387–D392
O'Malley R, Echer J (2010) Linking genotype to phenotype using the Arabidopsis unimutant collection. Plant J 61:928–940
The OpenScience Project (2010) Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/
The UniProt Consortium (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res 42:D191–D198
Vert G, Nemhauser J, Geldner N, Hong F, Chory J (2005) Molecular mechanisms of steroid hormone signaling in plants. Annu Rev Cell Dev Biol 21:177–201
Wainreb G, Wolf L, Ashkenazy H, Dehouck Y, Ben-Tal N (2011) Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site. Bioinformatics 27:3286–3292
Zhang H, Xu C, He Y, Zong J, Yang X, Si H, Sun Z, Hu J, Liang W, Zhang D (2013) Mutation in CSA creates a new photoperiod-sensitive genic male sterile line applicable for hybrid rice seed production. Proc Natl Acad Sci U S A 110:76–81