MtDB: a database for personalized data mining of the model legume Medicago truncatula transcriptome.
In order to identify the genes and gene functions that underlie key aspects of legume biology, researchers have selected the cool season legume Medicago truncatula (Mt) as a model system for legume research. A set of >170 000 Mt ESTs has been assembled based on in-depth sampling from various developmental stages and pathogen-challenged tissues. MtDB is a relational database that integrates Mt transcriptome data and provides a wide range of user-defined data mining options. The database is interrogated through a series of interfaces with 58 options grouped into two filters. In addition, the user can select and compare unigene sets generated by different assemblers: Phrap, Cap3 and Cap4. Sequence identifiers from all public Mt sites (e.g. IDs from GenBank, CCGB, TIGR, NCGR, INRA) are fully cross-referenced to facilitate comparisons between different sites, and hypertext links to the appropriate database records are provided for all queries' results. MtDB's goal is to provide researchers with the means to quickly and independently identify sequences that match specific research interests based on user-defined criteria. The underlying database and query software have been designed for ease of updates and portability to other model organisms. Public access to the database is at http://www.medicago.org/MtDB.
Lamblin
Anne-Françoise J
AF
Center for Computational Genomics and Bioinformatics, University of Minnesota, MMC43, 420 Delaware Street S.E., Minneapolis, MN 55455, USA.
Crow
John A
JA
Johnson
James E
JE
Silverstein
Kevin A T
KA
Kunau
Timothy M
TM
Kilian
Alan
A
Benz
Diane
D
Stromvik
Martina
M
Endré
Gabriella
G
VandenBosch
Kathryn A
KA
Cook
Douglas R
DR
Young
Nevin D
ND
Retzel
Ernest F
EF
D002874:Chromosome Mapping; D003196:Computer Graphics; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D018745:Genome, Plant; D016247:Information Storage and Retrieval; D029902:Medicago / Q000235:genetics*; D012984:Software; D014158:Transcription, Genetic; D014584:User-Computer Interface
D005819:Genetic Markers