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:
    • Search LIS data collections of QTL publications.
    • Search recent legume publications from Pubmed
• 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:

  • QTL search to Gbrowse

  • Gene search to phylotree to genome context viewer

  • Phylotree

  • Genome Context Viewer

  • Germplasm Map

FAQ

How can I view my data Gbrowse?

Gbrowse allows you to add your own data as a 'Custom Tracks' in a variety of file formats including SAM or BAM, GFF and GFF3.

Adding Custom Tracks

To upload your data, click on the 'Custom Tracks' tab and click on the link on the bottom for the source of the data you wish to add to Gbrowse. All tracks can be edited in the browser by clicking the '[edit]' link to the right of the file you wish to modify. A text box will appear where you can make changes, then click 'submit' to save your edits.

Uploaded Tracks

Click '[From a file]' to the right of the phrase Add custom tracks:. Click 'Choose File' to browse for the file you want to upload to Gbrowse. Click on 'Upload' to start the upload or 'Remove' to remove the upload box or cancel the upload process. The file will upload to the server and the screen will refresh once the upload is finished. If you want to overwrite the file you already uploaded, check the box beside 'If this file exists, overwrite it'.

Remove Tracks and URLs

Click '[From a URL]' to the right of the phrase Add custom tracks:. Paste the URL into the text box and click 'Import' to start the upload. If you know that the file has changed at the URL, click the '[reload]' link beside the source file and it will be updated.

Create Tracks

Click '[From text]' to the right of the phrase Add custom tracks:. Start typing the track information in the text box that appears, using one of the supported file formats. Once you are done, click 'Upload', Gbrowse will determine which file format you created and upload it.

Can I download track data from Gbrowse?

It is possible to download the track information from Gbrowse. All Gbrowse files available for download on LIS are in GFF3 file format. Recommendation: Do not open a gff3 file using Microsoft word or Microsoft excel. Recommend programs: Windows: Notepad++, Apple: TextWrangler

Information about the Gbrowse track

To view more information about the Gbrowse track and/or download the track information, click on the red question mark shown in the red circle in the figure above.

Download all data from Gbrowse track

After clicking the red question mark associated with the Gbrowse track of interest a box will appear. This box contains information about the track and a link to download the track data. Click on 'Download ALL DATA for this track' to download the data. To close the box click on the 'X' on the top right corner of the box.

Is there citation information about tracks in Gbrowse?

Citation information about the Gbrowse track

To view citation information about the Gbrowse track, click on the red question mark shown in the red circle in the figure above.

After clicking the red question mark associated with the Gbrowse track of interest a box will appear. This box contains information about the track, including the citation information. To close the box click on the 'X' on the top right corner of the box.

Can I find the coordinates of synteny features in Gbrowse, or navigate to the corresponding regions?

Information about how the synteny tracks were calculated

To view information about how the synteny track was calculated and what programs were used, click on the red question mark shown in the red circle in the figure above.

After clicking the red question mark associated with the synteny Gbrowse track of interest an information box will appear. This box contains information about the track, including a link to download the data associated with the track (red arrow) and it shows the methods used to calculate the synteny, and which species genome version was used (green box) . To close the box click on the 'X' on the top right corner of the box.

Coordinates of synteny features

After clicking on the interested synteny feature (example circled in red above) a GBrowse information box will appear. This box will contain the coordinates of the synteny feature chosen, the corresponding target genomic location, and median Ks. The box also contains a link that will direct you to the corresponding target genomic location, shown in the green box in the image above.

More information about the synteny features is available here.

How do I find the promotor for my gene of interest using GBrowse?

View the gene in GBrowse

Using your computer mouse, drag and select the region upstream your gene of interest under the lower GBrowse ruler.

Choose "Dump selection as FASTA" (red arrow). The upstream region can be downloaded for analysis on your local computer.

How do I find the promotor for my gene of interest using the Legume Mines?

Use the search utility at the top left for your gene of interest and the result would have a link in the Details column.

The Details link would take you to a gene page which has a number of details about this gene including JBrowse, Legume Gene Family, GO Annotation, Exon Features and Upstream/Downsteam Intergenic Region.

The 'Upstream Intergenic Region' (red arrow) can be found near the bottom of the page and the FASTA is available for download (red box). Multiple sections within the gene detail page have FASTA available for various features.