An expression database for roots of the model legume Medicago truncatula under salt stress
Manual Documents
The Medicago Truncatula Transporter database (MTDB) is a database of protein sequences of transporters of the model legume Medicago truncatula. The database is available to the public. Both automated search and manual curation were performed in identifying candidate protein sequences. Extensive annotations referring to each protein were generated, including basic protein function, genome locus, sequence annotations, 3D structure predict, as well as transmembrane segment and domain annotation. A chromosome distribution map, text-based and BLAST search tools against known sequences of M.truncatula and known 3D structures of transporters were also created. A user-friendly web interface and regular updates make MTDB valuable to researchers in related fields. We further provided a way to explore expression of M.truncatula transporter genes under stress treatments.

Home page

Users can check news or notifications of MTDB at the home page. Seven fundamental functions are available at left frame of web page. The browse and document parts have more than one selection.

Search page

Using the search function, for example, searching one type of transporters, or specifying certain inquiries like gene family, transporter name or MtID (Medicago truncatula ID). In addition, a batch search function is achieved, through which users can search the transporters information by inputting a set of MtIDs. The association with a brief summary on the page can provide users a useful platform for searching.

Transporter type

User can select one of the 7 types, and then all families belonged to the type are available on the page.

In order to make browsing more convenient and scientific, we make phylogenetic tree analysis to each family. Individual members of the families were further clustered and color-coded, based on the result of phylogenetic analysis . Each group contains links to individual protein pages.

Each group contains links to individual protein pages.

Each transport protein is presented in separate web pages where users can find detailed information such as transporter function annotation, TC classification, transmembrene segment prediction by TMHMM, genomic locus information, domain annotation prediction by Pfam, 3D structure predict, expression annotation, protein/cDNA/genome sequence, etc.

Distribution map

The chromosome map containing gene loci located on the chromosomal linkages were generated and visualized using GenomePixelizer, which give users a direct scope to the distribution of M.truncatula’s transporter genes on chromosomes and are especially useful in observing tandem duplications.

Advanced tools
In the function of the Advanced tools, three sections are included, Structure, Transmembrane Segment and Expression.