TY - JOUR
T1 - MIPS PlantsDB
T2 - A database framework for comparative plant genome research
AU - Nussbaumer, Thomas
AU - Martis, Mihaela M.
AU - Roessner, Stephan K.
AU - Pfeifer, Matthias
AU - Bader, Kai C.
AU - Sharma, Sapna
AU - Gundlach, Heidrun
AU - Spannagl, Manuel
PY - 2013/1/1
Y1 - 2013/1/1
N2 - The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/ genomes.jsp) was initially described in NAR in 2007 [Spannagl, M., Noubibou, O., Haase, D., Yang, L., Gundlach, H., Hindemitt, T., Klee, K., Haberer, G., Schoof, H. and Mayer, K.F. (2007) MIPSPlantsDB-plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834-D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB.
AB - The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/ genomes.jsp) was initially described in NAR in 2007 [Spannagl, M., Noubibou, O., Haase, D., Yang, L., Gundlach, H., Hindemitt, T., Klee, K., Haberer, G., Schoof, H. and Mayer, K.F. (2007) MIPSPlantsDB-plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834-D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB.
UR - http://www.scopus.com/inward/record.url?scp=84876548209&partnerID=8YFLogxK
U2 - 10.1093/nar/gks1153
DO - 10.1093/nar/gks1153
M3 - Article
C2 - 23203886
AN - SCOPUS:84876548209
SN - 0305-1048
VL - 41
SP - D1144-D1151
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -