ProtAnnDB
Sub-cellular localization
SignalP Improved prediction of signal peptides: SignalP 3.0.
JD Bendtsen, H Nielsen, G von Heijne and S Brunak
J. Mol. Biol., 340: 783-795, 2004.
Prediction of signal peptides and signal anchors by a hidden Markov model.
H Nielsen and A Krogh
Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB 6).
AAAI Press, Menlo Park, California, pp. 122-130, 1998.
TargetP Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.
O Emanuelsson, H Nielsen, S Brunak and G von Heijne
J. Mol. Biol., 300: 1005-1016, 2000.
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
H Nielsen, J Engelbrecht, S Brunak and G von Heijne
Protein Engineering, 10: 1-6, 1997.
LocTree3 LocTree3 prediction of localization.
Goldberg T, Hecht M, Hamp T, Karl T, Yachdav G, Ahmed N, Altermann U, Angerer P, Ansorge S, Balasz K, Bernhofer M, Betz A, Cizmadija L, Do KT, Gerke J, Greil R, Joerdens V, Hastreiter M, Hembach K, Herzog M, Kalemanov M, Kluge M, Meier A, Nasir H, Neumaier U, Prade V, Reeb J, Sorokoumov A, Troshani I, Vorberg S, Waldraff S, Zierer J, Nielsen H, Rost B.
Nucleic Acids Research, W350-5, 2014.
TMHMM A hidden Markov model for predicting transmembrane helices in protein sequences.
E Sonnhammer, G von Heijne and A Krogh
Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB98), 175-182, 1998.
Predotar Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences.
I Small, N Peeters, F Legeai and C Lurin
Proteomics, 4: 1581-1590, 2004.
Aramemnon ARAMEMNON, a novel database for Arabidopsis integral membrane proteins.
R Schwacke, A Schneider, E Van der Graaff, K Fischer, E Catoni, M Desimone, WB Frommer, UI Flügge and R Kunze
Plant Physiol, 131: 16-26, 2003.
GPI-SOM Identification of GPI anchor attachment signals by a Kohonen self-organizing map.
N Fankhauser and P Mäser
Bioinformatics, 21: 1846-1852, 2005.
PredGPI PredGPI: a GPI-anchor predictor.
A Pierleoni, PL Martelli and R Casadio
BMC Bioinformatics, 9:392, 2008.
Functional domains
Pfam The Pfam protein families database: towards a more sustainable future
RD Finn, P Coggill, RY Eberhardt, SR Eddy, J Mistry, AL Mitchell, SC Potter, M Punta, M Qureshi, A Sangrador-Vegas, GA Salazar, J Tate and A Bateman
Nucleic Acids Research, 44(D1): D279-D285, 2016.
The Pfam protein families database
RD Finn, J Tate, J Mistry, PC Coggill, JS Sammut, HR Hotz, G Ceric, K Forslund, SR Eddy, EL Sonnhammer and A Bateman
Nucleic Acids Research, Database Issue 36: D281-D288, 2008.
InterPro The InterPro protein families database: the classification resource after 15 years
A Mitchell, HY Chang, L Daugherty, M Fraser, S Hunter, R Lopez, C McAnulla, C McMenamin, G Nuka, S Pesseat, A Sangrador-Vegas, M Scheremetjew, C Rato, SY Yong, A Bateman, M Punta, TK Attwood, CJ Sigrist, N Redaschi, C Rivoire, I Xenarios, D Kahn, D Guyot, P Bork, I Letunic, J Gough, M Oates, D Haft, H Huang, DA Natale, CH Wu, C Orengo, I Sillitoe, H Mi, PD Thomas, RD Finn
Nucleic Acids Research, Database issue 43: D213-221, 2015.
InterProScan: protein domains identifier.
E Quevillon, V Silventoinen, S Pillai, N Harte, N Mulder, R Apweiler and R Lopez
Nucleic Acids Research, 33: W116-120, 2005.
The InterPro database, an integrated documentation resource for protein families, domains and functional sites
The InterPro Consortium
Nucleic Acids Research 29: 37-40, 1999.
Prosite The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases
SIB Swiss Institute of Bioinformatics Members
Nucleic Acids Research 44(D1): D27-D37, 2016.
New and continuing developments at PROSITE
CJ Sigrist, E de Castro, L Cerutti, BA Cuche, N Hulo, A Bridge, L Bougueleret and I Xenarios
Nucleic Acids Research, Database issue 41: D344-347, 2013.
The 20 years of PROSITE.
N Hulo, A Bairoch, V Bulliard, L Cerutti, BA Cuche, E de Castro, C Lachaize, PS Langendijk-Genevaux and CJ Sigrist
Nucleic Acids Research 36: D245-D249, 2008.
Protein sequences
NCBI RefSeq NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.
KD Pruitt, T Tatusova and DR Maglott
Nucleic Acids Res., 34: D61-D65, 2007.
TAIR Using the Arabidopsis Information Resource (TAIR) to find information about Arabidopsis genes.
L Reiser and ST Rhee
Curr Protoc Bioinformatics, 1.11, 2007.
Phytozome Phytozome: a comparative platform for green plant genomics.
DM Goodstein, S Shu, R Howson, R Neupane, RD Hayes, J Fazo, T Mitros, W Dirks, U Hellsten, N Putnam, DS Rokhsar
Nucleic Acids Res, 40(Database issue): D1178-1186, 2012.
MaiZEGDB MaizeGDB: The maize model organism database for basic, translational, and applied research.
Lawrence CJ, Harper LC, Schaeffer ML, Sen TZ, Seigfried TE, Campbell DA
Int J Plant Genomics, Volume 2008 (2008), Article ID 496957, 2008.
Databases
Planet PlaNet: combined sequence and expression comparisons across plant networks derived from seven species
M Mutwil, S Klie, T Tohge, FM Giorgi, O Wilkins, MM Campbell, AR Fernie, B Usadel, Z Nikoloski and S Persson
Plant Cell 23: 895-910, 2011.
Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm.
M Mutwil, B Usadel, M Schütte, A Loraine, O Ebenhöh and S Persson
Plant Physiol., 152:29-43, 2010.
Uniprot UniProt: a hub for protein information
The UniProt Consortium
Nucleic Acids Res.43: D204-D212, 2015.
Peroxibase PeroxiBase: a database for large-scale evolutionary analysis of peroxidases.
N Fawal, Q Li, B Savelli, M Brette, G Passaia, M Fabre, C Mathé, C Dunand
Nucleic Acids Res.41(Database issue):D441-444, 2013.
WallProtDB WallProtDB, a database resource for plant cell wall proteomics
H San Clemente and E Jamet
Plant Methods 11: 2, 2015.