POGs2: A web portal to facilitate cross-species inferences about protein architecture and function in plants

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Tomcal, Michael ^a   Stiffler, Nicholas ^a   Barkan, Alice ^a  

^a UNIVERSITY OF OREGON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; VEGETABLE PROTEIN;

ACCESS TO INFORMATION; ARABIDOPSIS THALIANA; ARTICLE; CELLULAR DISTRIBUTION; COMPUTER INTERFACE; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC ANALYSIS; INFORMATION PROCESSING; INTERNET; MAIZE; MOLECULAR CLONING; MULTIGENE FAMILY; NONHUMAN; ORTHOLOGY; PARALOGY; POPULUS TRICHOCARPA; PREDICTION; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTEOMICS; PUTATIVE ORTHLOGOUS GROUPS 2 DATABASE; QUANTITATIVE TRAIT LOCUS MAPPING; REFERENCE DATABASE; RICE; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; TRANSPOSON; VALIDITY;

ALGORITHMS; ARABIDOPSIS; DATABASES, NUCLEIC ACID; ORYZA SATIVA; POPULUS; SEQUENCE ANALYSIS, DNA; ZEA MAYS;

EID: 84892426529     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0082569     Document Type: Article

References (22)

1. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD et al. (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40: D1178-D1186. doi:10.1093/nar/gkr944. PubMed: 22110026.
2. Jaiswal P (2011) Gramene database: a hub for comparative plant genomics. Methods Mol Biol 678: 247-275. PubMed: 20931385.
3. Rouard M, Guignon V, Aluome C, Laporte MA, Droc G et al. (2011) GreenPhylDB v2.0: comparative and functional genomics in plants. Nucleic Acids Res 39: D1095-D1102. doi:10.1093/nar/gkq847. PubMed: 20864446.
4. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M et al. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35: D883-D887. doi:10.1093/nar/gkl976. PubMed: 17145706.
5. Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C et al. (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40: D1202-D1210. doi:10.1093/nar/gkr1090. PubMed: 22140109.
6. Sen TZ, Andorf CM, Schaeffer ML, Harper LC, Sparks ME et al. (2009) MizeGDB becomes 'sequence-centric'. Database (Oxford). p. bap020. PubMed: 21847242
7. Walker NS, Stiffler N, Barkan A (2007) POGs/PlantRBP: a resource for comparative genomics in plants. Nucleic Acids Res 35: D852-D856. doi:10.1093/nar/gkl795. PubMed: 17142226.
8. Trachana K, Larsson TA, Powell S, Chen WH, Doerks T et al. (2011) Orthology prediction methods: a quality assessment using curated protein families. Bioessays 33: 769-780. doi:10.1002/bies.201100062. PubMed: 21853451.
9. Flicek P, Amode MR, Barrell D, Beal K, Brent S et al. (2011) Ensembl 2011. Nucleic Acids Res 39: D800-D806. doi:10.1093/nar/gkq1064. PubMed: 21045057.
10. Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R et al. (2009) EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 19: 327-335. PubMed: 19029536.
11. Van Bel M, Proost S, Wischnitzki E, Movahedi S, Scheerlinck C et al. (2012) Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiol 158: 590-600. doi:10.1104/pp.111.189514. PubMed: 22198273.
12. Li L, Stoeckert CJ Jr., Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178-2189. doi:10.1101/gr.1224503. PubMed: 12952885.
13. Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK et al. (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res 40: D306-D312. doi:10.1093/nar/gkr948. PubMed: 22096229.
14. Sun Q, Zybailov B, Majeran W, Friso G, Olinares PD et al. (2009) PPDB, the Plant Proteomics Database at Cornell. Nucleic Acids Res 37: D969-D974. doi:10.1093/nar/gkn654. PubMed: 18832363.
15. Emanuelsson O, Brunak S, von Heijne G, Nielsen H (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2: 953-971. doi:10.1038/nprot.2007.131. PubMed: 17446895.
16. Small I, Peeters N, Legeai F, Lurin C (2004) Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 4: 1581-1590. doi:10.1002/pmic.200300776. PubMed: 15174128.
17. Brameier M, Krings A, MacCallum RM (2007) NucPred - predicting nuclear localization of proteins. Bioinformatics 23: 1159-1160. doi:10.1093/ bioinformatics/btm066. PubMed: 17332022.
18. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797. doi:10.1093/nar/gkh340. PubMed: 15034147.
19. Smits SA, Ouverney CC (2010) jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web. PLOS ONE 5: e12267. doi:10.1371/journal.pone.0012267. PubMed: 20805892.
20. Brown NP, Leroy C, Sander C (1998) MView: a web-compatible database search or multiple alignment viewer. Bioinformatics 14: 380-381. doi:10.1093/bioinformatics/14.4.380. PubMed: 9632837.
21. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402. doi:10.1093/nar/25.17.3389. PubMed: 9254694.
22. Williams-Carrier R, Stiffler N, Belcher S, Kroeger T, Stern DB et al. (2010) Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize. Plant J 63: 167-177. PubMed: 20409008.