LegumeDB

Legume-specific Bioinformatics Resource for Legume Researchers

LegumeDB is a web-based bioinformatics resource for comparative genomic analysis developed at the CCG. This curated resource enables data storage and visualization of numerous sequence analyses (and re-analyses) from diverse / customized database sets and alignment programs.

Features such sequence alignments, genes and markers can be integrated and visualized in LegumeDB's genetic and physical comparative maps.

LegumeDB in-silico markers can be designed spanning intron and SSR regions in genomic and cDNA based on conserved sequence alignments with a number of different legume species (contact enquiries@ccg.murdoch.edu.au for help with your analysis).

SOE BLAST - Comparative Sequence Viewer

Users will have the option to screen sequence(s) against the LegumeDB databases and subdata sets with a number of alignment algorithms. All analyses are stored in a database and results can be viewed concurrently in the SOE comparative Sequence Viewer. Password Restricted Accounts Available.

submitSequence(s)

LegumeDB CMap - Comparative Map Viewer

CMap is a web-based tool that allows users to view comparisons of genetic and physical maps in the model and agronomic important legume species. The package also includes tools for curating map data ([1]). Password Restriction.

Retrieve Genbank Sequences - Using GenBankBatch

GenBankBatch is an web based application to retrieve GenBank sequence(s) from a list of genbank accession numbers (gb) or genbank id numbers (gi). The user can choose to type or paste the list into the web form or upload a file containing the list. No access Restrictions required.

PubMatrix literature Retrieval

PubMatrix compares any list of terms against any other list of terms in PubMed. It reports the frequency of co-occurrence between all pairwise comparisons between the two lists as a matrix table. The user can then sort or browse the frequency matrix table to do individual searches. The PubMatrix database archives previous searches. Registration Required.

LegumeDB resource tools examples

Reference:

(2005) LegumeDB bioinformatics resource: Comparative genomic analysis and novel cross-genera marker identification in Lupin and pasture legume species P. Moolhuijzen, M. Cakir, A Macgregor, C Smith, A. Hunter, D. Schibeci, M. Francki , M Jones, R. Appels, M. Bellgard (In Press Genome)