References

Tools
  1. InterPro [link]
    Sarah Hunter et al. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Research 40, 306–312 (2012).
  2. DROP [link]
    Teppei Ebina et al. DROP: an SVM domain linker predictor trained with optimal features selected by random forest. BIOINFORMATICS 27, 487–494 (2010).
  3. Plant O-glycosylation [link]
    Veronique Gomord et al. Plant-specific glycosylation patterns in the context of therapeutic protein production. Plant Biotechnology Journal 8, 564–587 (2010).
  4. UbPred [link]
    Radivojac, P. et al. Identification, Analysis and Prediction of Protein Ubiquitination Sites. Proteins 78, 365–380 (2010).
  5. SOLpro [link]
    Christophe N. Magnan et al. SOLpro: accurate sequence-based prediction of protein solubility. Bioinformatics 25, 2200–2207 (2009).
  6. WoLF PSORT [link]
    Yang, L. et al. WoLF PSORT: protein localization predictor. Nucleic Acids Research 35, 585–587 (2007).
  7. DIpro [link]
    J. Cheng et al. Large-Scale Prediction of Disulphide Bridges Using Kernel Methods, Two-Dimensional Recursive Neural Networks, and Weighted Graph Matching. Proteins 62, 617–629 (2006).
  8. RONN [link]
    Zheng Rong Yang et al. RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins. Bioinformatics 21, 3369–3376(2005).
  9. NetNGlyc [link]
    R. Gupta, E. Jung and S. Brunak. Prediction of N-glycosylation sites in human proteins. In preparation (2004).
  10. ProteoMix [link]
    E. Chikayama et al. ProteoMix: an integrated and flexible system for interactively analyzing large numbers of protein sequences Bioinformatics 20, 2836–2838 (2004).
  11. Accpro, SSpro  [link]
    J. Cheng et al. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Research 33, 72–76 (2002).
  12. TMHMM [link]
    Sun, J. et al. Predicting Transmembrane Protein Topology with a Hidden Markov model: Application to Complete Genomes. Journal of Molecular Biology 305, 567–580 (2001).
  13. KOG [link]
    Tatusov RL. et al. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33–6 (2000).
  14. PASS  [link]
    Y. Kuroda et al. Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics. Protein Science 9, 2313–2321 (2000).
  15. TargetP [link]
    Olof Emanuelsson et al. Predicting Subcellular Localization of Proteins Based on their N-terminal Amino Acid Sequence. J. Mol. Biol 300, 1005–1016 (2000).
  16. SignalP [link]
    Henrik Nielsen et al. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Engineering 12, 3–9 (1999).
Resources
  1. Arabidopsis [link]
    Swarbreck D. et al. The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Research 36, D1009–1014 (2008).
  2. Soybean
    Schmutz J. et al. Genome sequence of the palaeopolyploid soybean. Nature 463, 178–183 (2010).
  3. Poplar
    Tuskan GA. et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 1596–1604 (2006).
  4. Rice (MSU) [link]
    Ouyang S. et al. The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Research 35, D883–887 (2007).
  5. Rice (RAP) [link]
    Ohyanagi H. et al. The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucleic Acids Research 34, D741–D744 (2006).
  6. RAP-DB (rice) [link]
    Ohyanagi H. et al. Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Research 17, 175–183 (2007).
  7. Moss
    Rensing SA. et al. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319, 64–69 (2008).
  8. Algae [link]
    Matsuzaki M. et al. Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428, 653–657 (2004).
  9. Mouse [link]
    Robert H. Waterston et al. Initial sequencing and comparative analysis of the mouse genome Mouse Genome Sequencing Consortium. Nature 420, 520–562 (2002).
  10. Yeast [link]
    H. W. Mewes et al. MIPS: a database for protein sequences, homology data and yeast genome information. Nucleic Acids Research 25, 28–30 (1997).
    H. W. Mewes et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Research 30, 31–34 (2002).
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