Plant genomic information:

• 1. NCBI
  Tatusova, T., Smith-White, B. and Ostell, J. (2007) A collection of plant-specific genomic data and resources at NCBI. Methods in molecular biology, 406, 61-87.
• 2. TAIR
  Rhee, S.Y., Beavis, W., Berardini, T.Z., Chen, G., Dixon, D., Doyle, A., Garcia-Hernandez, M., Huala, E., Lander, G., Montoya, M. et al. (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic acids research, 31, 224-228.
• 3. TIGR (currently named the J. Craig Venter Institute) Rice Genome Annotation Project
  Ouyang, S., Zhu, W., Hamilton, J., Lin, H., Campbell, M., Childs, K., Thibaud-Nissen, F., Malek, R.L., Lee, Y., Zheng, L. et al. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic acids research, 35, D883-887.

MicroRNA databases:

• 1. miRBase
  Griffiths-Jones, S., Grocock, R.J., van Dongen, S., Bateman, A. and Enright, A.J. (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic acids research, 34, D140-144.
• 2. PMRD
  Zhang, Z., Yu, J., Li, D., Zhang, Z., Liu, F., Zhou, X., Wang, T., Ling, Y. and Su, Z. (2009) PMRD: plant microRNA database. Nucleic acids research, 10.1093/nar/gkp818

Microarray or high-throughput sequencing data:

• 1. GEO
  Barrett, T., Troup, D.B., Wilhite, S.E., Ledoux, P., Rudnev, D., Evangelista, C., Kim, I.F., Soboleva, A., Tomashevsky, M., Marshall, K.A. et al. (2009) NCBI GEO: archive for high-throughput functional genomic data. Nucleic acids research, 37, D885-890.
  Edgar, R., Domrachev, M. and Lash, A.E. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic acids research, 30, 207-210.
• 2. ASRP
  Gustafson, A.M., Allen, E., Givan, S., Smith, D., Carrington, J.C. and Kasschau, K.D. (2005) ASRP: the Arabidopsis Small RNA Project Database. Nucleic acids research, 33, D637-640.
• 3. CSRDB
  Johnson, C., Bowman, L., Adai, A.T., Vance, V. and Sundaresan, V. (2007) CSRDB: a small RNA integrated database and browser resource for cereals. Nucleic acids research, 35, D829-833.
• 4. Plant MPSS databases
  Nakano, M., Nobuta, K., Vemaraju, K., Tej, S.S., Skogen, J.W. and Meyers, B.C. (2006) Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic acids research, 34, D731-735.
• 5. CSPSR

Target prediction:

• 1. Target Finder
  Allen, E., Xie, Z., Gustafson, A.M. and Carrington, J.C. (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell, 121, 207-221.
  Fahlgren, N., Howell, M.D., Kasschau, K.D., Chapman, E.J., Sullivan, C.M., Cumbie, J.S., Givan, S.A., Law, T.F., Grant, S.R., Dangl, J.L. et al. (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PloS one, 2, e219.
• 2. miRU
  Zhang, Y. (2005) miRU: an automated plant miRNA target prediction server. Nucleic acids research, 33, W701-704.
• 3. psRNATarget
  Dai and Zhao, paper under preparation.
• 4. Tool provided by CSRDB
  Johnson, C., Bowman, L., Adai, A.T., Vance, V. and Sundaresan, V. (2007) CSRDB: a small RNA integrated database and browser resource for cereals. Nucleic acids research, 35, D829-833.

Target function analysis:

• GO::TermFinder
  Boyle, E.I., Weng, S., Gollub, J., Jin, H., Botstein, D., Cherry, J.M. and Sherlock, G. (2004) GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics, 20, 3710-3715.

Secondary structure prediction:

• RNAfold
  Hofacker, I.L. (2003) Vienna RNA secondary structure server. Nucleic acids research, 31, 3429-3431.

Promoter analysis:

• 1. PlantProm
  Shahmuradov, I.A., Gammerman, A.J., Hancock, J.M., Bramley, P.M. and Solovyev, V.V. (2003) PlantProm: a database of plant promoter sequences. Nucleic acids research, 31, 114-117.
• 2. TSSP
  Shahmuradov, I.A., Gammerman, A.J., Hancock, J.M., Bramley, P.M. and Solovyev, V.V. (2003) PlantProm: a database of plant promoter sequences. Nucleic acids research, 31, 114-117.
• 3. PlnTFDB
  Riano-Pachon, D.M., Ruzicic, S., Dreyer, I. and Mueller-Roeber, B. (2007) PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics, 8, 42.
• 4. PlantTFDB
  Guo, A.Y., Chen, X., Gao, G., Zhang, H., Zhu, Q.H., Liu, X.C., Zhong, Y.F., Gu, X., He, K. and Luo, J. (2008) PlantTFDB: a comprehensive plant transcription factor database. Nucleic acids research, 36, D966-969.
• 5. WebLogo
  Crooks, G.E., Hon, G., Chandonia, J.M. and Brenner, S.E. (2004) WebLogo: a sequence logo generator. Genome research, 14, 1188-1190.
• 6. PLACE
  Higo, K., Ugawa, Y., Iwamoto, M. and Higo, H. (1998) PLACE: a database of plant cis-acting regulatory DNA elements. Nucleic acids research, 26, 358-359.
  Higo, K., Ugawa, Y., Iwamoto, M. and Korenaga, T. (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic acids research, 27, 297-300.
• 7. PlantCARE
  Lescot, M., Dehais, P., Thijs, G., Marchal, K., Moreau, Y., Van de Peer, Y., Rouze, P. and Rombauts, S. (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic acids research, 30, 325-327.