Site Overview and Guide

Search Tools | Genomic & Genetic Tools | Germplasm | Data Submission | Website Tours | FAQ
Legume Information System is organized around these features and tools:
  • Genome browsers: We have both GBrowse and JBrowse genome browsers for ten legume species. Three more legume genome browsers are available at our sister sites: Soybase and Peanutbase.
  • Data Store: Data sets for download. More added regularly. Let us know if you have data to contribute, or if you need particular data sets; we may be able to point you to the resources elsewhere, or prioritize making these available at the Data Store.
  • Legume Federation: not part of this website, but important as a listing of related legume projects and on-line tools. Also see the Community page on this site, for links to other resources.
  • Trait & Maps: LIS maintains a (growing) collection of genetic maps, description about the genetic maps, and many with genetic maps QTL features. We collect published legume QTL information and integrate it into a common genetic framework. This data can be searched by QTL symbol (i.e. Pup4.1) or by trait class.

    Tour: QTL search -> Gbrowse

  • Search tools:
    • BLAT: You can conduct a BLAT search using either DNA or RNA as the query sequence. The query sequence can be aligned to any of the eight legume genomes and the alignments will be displayed in the genome browser of the selected species. You can further filter the results by changing the number of returning hits and/or the minimum percent identity.
    • BLAST: You can conduct a BLAST search using either a nucleotide or protein query sequence. Select a target BLAST database and advanced BLAST search options are available.
    • Keyword search: Search GBrowse genome browser by entering terms to search for features (gene or marker names, functional descriptions, etc.) on the indicated genome. You will see the results displayed on a karyotpe view of chromosomes and in a list report. You can go from there to a detailed view of the features on the GBrowse genome browser.
    • Gene family search: Search for gene families starting from a family ID (e.g. phytozome_10_2.59192412), using words from the family description (e.g., iron homeostasis or chlorophyll binding protein), or using the "count" filters to find families by size or species composition. [More detailed help]
    • Gene search: Search for genes with gene name (i.e. [Contains]: Glyma.15G005900 OR [Contains any word]: Medtr4g076850 Aradu.58KSZ; omit transcript suffixes, i.e. '.1') and/or Interpro domains (i.e. [Contains]: PF05659) and/or gene description (i.e. [Contains any word]: proteasome) and/or Phytozome gene families (i.e. [is equal to]: phytozome_10_2.59192412). [Guide for Gene Basket tool]

      Tour: Gene search -> phylotree -> genome context viewer

    • Genetic Maps search: There you can search LIS growing collection of genetic maps by map name or using words from the map description (i.e. seed coat).
    • Marker search: Search for markers in Phaseolus vulgaris (example markers: STS, microsatellite, intron_variant, conserved_region)
    • Protein domain search: Search for protein domains by using protein domain ID (i.e. [is equal to]: PF00139) and/or protein domain name (i.e. [Contains]: Zinc finger) and/or Interpro term (i.e. [is equal to]: IPR027278) and/or protein domain description search (i.e. [Contains all words]: disease resistance). You can also search by using the "count" filters to protein domains by size or species composition.
    • QTL search: You can search LIS QTL collection by trait class (i.e. yield or root) and/or by QTL symbol used in the experiment and/or by QTL symbol (i.e. Pod harvest or Seed weight).
    • Publication search:
  • Genomic and Genetic tools
    • Gene Basket/Bulk download: Click Add to Basket or Add all genes to Basket button. To view genes in the basket, click on Go to basket page. From this page you can bulk download polypeptide or mRNA sequences.
    • Phylotree: Click on colored terminal nodes to view more information about the individual gene. Click on white internal nodes to view Genomic Context Viewer for that legume subtree. Click on dark gray root node to view either the gene family Multiple Sequence Alignment or the Genomic Context Viewer for all legume species in that gene family.

      Tour: Phylotree

    • Genome Context viewer: The triangles with the thick border are the gene family you started from. The white triangles with a dashed border have no gene family assignment; white triangles with solid borders represent genes with family assignments that are not shared by other genes in the view. The list of other gene families and the colors representing them in the viewer are on the top right. The shade of the black/gray line between two triangles is indicative of the intergenic region length (i.e. light gray = short or overlapping; thick black = very long).

      Tour: Genome Context Viewer

    • Multiple Sequence Alignment viewer: On the top left of the screen under the word 'phytozome_10': click on tree to view the gene family tree; click on view to view the multiple sequence alignment; click on download to download the multiple sequence alignment; click on jalview to view the multiple sequence alignment using Jalview Tool [ Note: you must change Java settings to use Jalview. ]
  • Legume Germplasm Resources
    • GRIN Connect: Search for germplasm at USDA GRIN (NPGS) database. Use this utility if you want to search the entire USDA GRIN germplasm database from within LIS. You will be able to see and search the GRIN website within a LIS page with a GRIN accession number. You can also check, if it exists, the evaluation data for the germplasm accession from the 'Detailed Accession Observation Page' link in the GRIN webpage.
    • Trait Evaluation Data: Search for germplasm evaluation data. Germplasm evaluation data (for common crop traits or descriptors) for the following legumes are available via LIS from GRIN. The evaluation data sets have been downloaded from the GRIN website and are served here by LIS.
    • Geographic distribution of legume germplasm: Locate germplasm accession in a map. Legume germplasm accessions can be located on a map using a Geographical Information System (GIS) utility . You can search the distribution of germplasm accessions in a given geographic area, can map multiple species or restrict it to a single legume taxon, look at the accession details and evaluation data if available, and overlay trait evaluation data on the map.

      Tour: Germplasm Map

  • Data submission: there is a spreadsheet form available for describing QTL experiments, maps, and their publication. Data submissions we have received directly from researchers are extremely valuable, since a researcher knows the information intimately and is the expert on their work. If you are working on phenotyping or mapping, please feel free to download the form, and contact us with questions.

  • Website Tours: