MtDB: a database for personalized data mining of the model legume Medicago truncatula transcriptome.
ABSTRACT 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.
[show abstract] [hide abstract]
ABSTRACT: Molecular maps have been developed for many species, and are of particular importance for varietal development and comparative genomics. However, despite the existence of multiple sets of linkage maps, databases of these data are lacking for many species, including peanut. PeanutMap http://peanutgenetics.tamu.edu/cmap provides a web-based interface for viewing specific linkage groups of a map set. PeanutMap can display and compare multiple maps of a set based upon marker or trait correspondences, which is particularly important as cultivated peanut is a disomic tetraploid. The database can also compare linkage groups among multiple map sets, allowing identification of corresponding linkage groups from results of different research projects. Data from the two published peanut genome map sets, and also from three maps sets of phenotypic traits are present in the database. Data from PeanutMap have been incorporated into the Legume Information System website http://www.comparative-legumes.org to allow peanut map data to be used for cross-species comparisons. The utility of the database is expected to increase as several SSR-based maps are being developed currently, and expanded efforts for comparative mapping of legumes are underway. Optimal use of these data will benefit from the development of tools to facilitate comparative analysis.BMC Bioinformatics 02/2006; 7:375. · 2.75 Impact Factor
[show abstract] [hide abstract]
ABSTRACT: Because the expression levels of housekeeping genes are relatively constant in most tissues, they are often useful controls when quantifying gene expression. We present an analytical method for identifying candidate housekeeping controls using expressed sequence tags (ESTs) from The Institute for Genomic Research Tomato Gene Index. We found relative expression levels for a collection of 127 transcripts and calculated the percentage of cDNA libraries that had expression levels (for a given transcript) within 2-fold through 10-fold ranges. When all libraries were considered together, the highest ranked housekeeping controls included transcripts for a DanJ-like protein, translationally controlled tumor protein, two alpha-tubulins, cyclophilin, and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). For each organ (leaf, root, fruit, and flower), at least one transcript was found that occurred within a 2-fold range of expression in all respective libraries. These included transcripts for alpha-tubulin, DnaJ-like proteins, phosphoglycerate kinase, and GAPDH, although different transcripts appear better suited than others for different tissues. This analytical method is useful for identifying candidate housekeeping controls in particular tissues and at particular levels of expression and would be relevant for any species for which significant EST data exist.BioTechniques 11/2003; 35(4):740-2, 744, 746 passim. · 2.67 Impact Factor
Article: Comparative analysis of plant and animal models for characterization of Burkholderia cepacia virulence.[show abstract] [hide abstract]
ABSTRACT: A simple alfalfa model was developed as an alternative infection model for virulence studies of the Burkholderia cepacia complex. Symptoms of disease were observed in wounded alfalfa seedlings within 7 days following inoculation of 10(1) to 10(5) CFU of most strains of the B. cepacia complex. Strains from seven genomovars of the B. cepacia complex were tested for virulence in the alfalfa model, and the degree of virulence was generally similar in strains belonging to the same genomovar. Strains of Burkholderia multivorans and some strains of Burkholderia stabilis did not cause symptoms of disease in alfalfa seedlings. Representative strains were also tested for virulence using the rat agar bead model. Most of the strains tested were able to establish chronic lung infections; B. stabilis strains were the exception. Most of the strains that were virulent in the alfalfa infection model were also virulent in the lung infection model. The B. cepacia genomovar III mutants K56pvdA::tp and K56-H15 were significantly less virulent in the alfalfa infection model than their parent strain. Therefore, this alfalfa infection model may be a useful tool for assessing virulence of strains of the B. cepacia complex and identifying new virulence-associated genes.Infection and Immunity 10/2003; 71(9):5306-13. · 4.16 Impact Factor