Due to the emerging COVID-19 pandemic, JGI will not be accepting or processing any samples because of reduced onsite staffing until further notice.

If you have any issues or concerns then please do not hesitate to let us know about it.

Help Home > Search

browse tab higlighted within the navigation

Search

The JGI Genome Portal Search application is used to locate gene models of interest in portal genomes or genome groups. This tool has been completely overhauled in Portal 6.0 with a powerful new indexing engine under the hood and a flexible and intuitive new interface. Here we describe use of the Search tool.

screenshot of search

Specifying a gene search

screenshot of search entry

A gene model search is comprised of the following four options.

  1. Search terms
  2. Search by: search criteria
  3. Across: search range
  4. Sort: results sorting

Search terms

A gene model search begins by entering one or more search terms in the search text box. Multiple search terms are combined using a logical "and" meaning that a search for the terms pyruvate kinase will return only results containing both "pyruvate" and "kinase".

Search Criteria

Select from the Search By: options to search for genes based on:
  1. Keyword. Search terms will be matched against all of the criteria listed below, as well against other information associated with gene models (e.g. KEGG, KOG, and PFamm annotations).
  2. Track. Search for all genes from a track matching the search term. (Example: "FiltereModels1")
  3. Go Terms. Search for genes that have been assigned a given GO term.(Example: "GO:0005975")
  4. Go Terms and Descriptions. Search for all genes that have been assigned either a given GO term or a GO term whose description matches the search string.(Example: "GO:0005975" or "Carbohydrate Metabolism")
  5. Go Lineage. Search for genes that have been assigned a given GO term or have been assigned a GO term which is a child of the specified term. For instance, a Go Lineage search on "GO:0006520" (Cellular amino acid metabolic process) will return genes assigned with this term, as well as genes assigned with child terms such as GO:0006522 (Alanine metabolic process).
  6. Go Lineage and Descriptions. Search for that genes that have been assigned a GO term matching the given term/description or any child of such a term.
  7. Protein Id. If you know the JGI Protein Id of a given gene, use this option to find it directly.
  8. Transcript Id. If you know the JGI Transcript Id of a given gene, use this option to find it directly.

Search Range

Using the Across: options, you can limit your search to specific gene model tracks. Your choices are:
  • Gene Catalog. Search the current set of "blessed" gene models
  • Default Analysis Track. Search the model track chosen by the JGI for primary analysis.
  • All Models. Search all tracks.

Results Sorting

You may opt to sort your search hits:
  • by score. Search score is a numeric value representing the relevance of each match to the given query parameters. The higher the score, the better the match between the gene model and the query.
  • by gene name - ascending. Alphabetical ordering by gene name from A-Z.
  • by gene name - descending. Alphabetical ordering by gene name from Z-A.

Analyzing Search Results

When you hit the Search Button, the JGI search engine begins processing your request, spawning searches across multiple organisms (in the case of a genome group search) and tracks in parallel. In most cases, the search will be returned almost immediately and presented for your analysis in a results table, described below . In the case of a broad query (for instance, the keyword "kinase" across all tracks in all organisms in the group "fungi") the progress of the search will be displayed in a panel immediately above the results table. This is described in the section that follows.

Monitoring search progress and viewing summary results

The Search Status panel is found between the search controls dialog, and the results table. As your search is executing, the Search Status panel looks like this: search status panel screenshot: in progress The panel displays the accumulating number of models returned by the search ("records retrieved") and processed for display and summary statistics ("records processed"). Expand the Search Status panel by clicking on it. You will then see a summary table displaying the number of records searched and the number of records matched for each organism in the search: search status panel screenshot: expanded When the search is complete, the Search Status Panel will display "Search is completed" and the Search results table will be displayed (described below). search status panel screenshot: completed

The Search Results table

Below we see a row from the Search Results table for an example query, representing a single search match: search results table screenshot Each hit in the Search Results table provides the following information:
  • Score. Search score is a numeric value representing the relevance of each match to the given query parameters. The higher the score, the better the match between the gene model and the query.
  • Organism. A link to the JGI organism portal for the genome containing the hit.
  • Gene. The name of the gene, along with links to the gene's protein page, transcript annotation page, and location on the Genome Browser.
  • Gene Ontology. Links to GO terms assigned to the gene.
  • Interpro. Links to Interpro protein sequence motifs assigned to the gene.
  • Domains. Links to PFAM protein domains assigned to the gene.

Saving search results

search screenshot: downloading results The JGI Search tool allows you to save your gene search results in a variety of formats. Simply pick a file format and a compression format and click Download. File and compression formats are described below.

File formats

  • csv (comma-separated values). Each row is line with columns separated by columns. Use this format for import to Excel.
  • as protein FASTA. A FASTA file of the amino acid sequence.
  • as transcript FASTA. A FASTA file of the nucleic sequence (spliced - exons only).
  • as genomic FASTA. A FASTA file of the nucleic sequence (unspliced - including introns).

Compression formats

  • uncompressed. A FASTA file of the amino acid sequence.
  • compressed by GZip. Compressed using the GNU GZip format.
  • compressed by Zip. Compressed using the Zip format.

Access To Portal 5.0 Search tools

old search links

Some features, such as homology-based searching, have not yet been implemented in the new Search tool. For this reason, we are still providing access to our previous search tools, Basic Search and Advanced Search. Links to these tools can be found in the upper right corner of the search page. Note that these links will not appear on search pages for genome groups, which are not supported by the 5.0 search tools.