Tools Help

The search tool allows you to easily search the Hardwood Genomics website for data of interest. A simple search for chestnut yields the following results:

From here, we can click on the content types in the Filter By Category area on the right-hand side of the screen to narrow down our search.

Downloading Search Results

Once a search is performed, a "Create Downloadable Collection" button becomes available to save your results. After a collection is created, the results become available for download in multiple formats such as comma-separated (CSV) and FASTA (for genes only). Creating a collection requires a signed-in user. If you do not have an account, you can register here.

Advanced Search

Wildcard Search

You can use the asterisk symbol * to perform a wildcard search. Examples:

genom* sequence (matches: genome, genomic, genomics ...)
Lir*dron tulipifera (matches: Liriodendron tulipifera)

Fuzzy Search

When you don't know how to exactly spell the keywords, you can use fuzzy search. Fuzzy search allows you to search for similar words. You use the ~ character at the end of your keyword for fuzzy search (keyword~). Examples:

sequeeence~ (matches: sequence)
Alnus rhmifolia~ (matches: Alnus rhombifolia)

Combining Queries

AND, OR, NOT operator and combination search. Examples:

"heat stress" AND ("Castanea mollissima" OR "green ash") NOT "heat shock"

Boolean Operators

+ and -. + means must be present; - means must not be present

Examples:

+"green ash" +transcriptome -genome (excludes the word genome)
+"green ash" -transcriptome +genome (includes the word genome)

The expression visualization tools allow you to explore and visualize expression data produced by microarray or RNAseq experiments.

Feature comparison heatmap

Clicking on the Expression Visualization tool link will bring you to a feature search page. This page allows you to input feature names to produce a heatmap comparing the expression data available for those features.

You can enter feature names in the box on the left, or, you can use the search box on the right to search for features. As you find features of interest, click on them to populate your comparison.

Once you are satisfied, click the Display Expression Heatmap button to generate a map with the chosen features. Expression data is organized by Analysis: there may be multiple expression analyses for a given organism, so be sure to check the dropdown box.

An expression experiment consists of multiple biological samples (NCBI biosamples) which were exposed to varying treatments or conditions. The RNA from those samples was harvested and an RNA-seq experiment was performed, with reads mapped to the reference assembly and subsequent statistical analyses performed, resulting in normalized read counts for each biosample for each feature.

The heatmap conveys this information by displaying the biosamples in that experiment along the X-axis, and the chosen features along the Y-axis.

You can hover the mouse over an individual cell of the heatmap to get more information about that biosample. This will include the tissue type and treatment of that biosample, as well as other experimental or environmental properties.

Downloading Data

You can download the expression data for your selected features by clicking on the green Download expression data button at the bottom of the plot.

You can also save a picture of your current plot in .png format by clicking on the camera icon in the upper right of the plot.

Individual feature

Expression data can also be displayed for an individual feature by clicking on the Expression pane, when available. Note that this plot will only display results for a single feature. If many samples are included in the analysis, the plot size may be greater than your display, and the plot will be scrollable along the X-axis.

To use the tool, you must first select an analysis, as there may be multiple expression analyses for a single feature. You can also select a property to sort and color the plot by. These properties correspond to the different property values of the biosamples. In the below example, the data is sorted by temperature, and colored by biosample age. Note that the group labels along the X-axis describe the temperature value: 4C or Ambient.

You can hover over each biosample to view all of the property values associated with it, as well as the exact expression value.

Manipulating the plot

In addition to choosing the sorting and coloring properties, you can manipulate the location of the groups and legend for your plot. Click on any group to drag it: move it beyond another group to swap their position. You may also click and drag the legend to change its position.

Biosamples with a value of 0 are included in the plot by default. You may press the Only Non-Zero Values button in the upper left of the plot to remove them. Press the Reset button to revert the plot to its original configuration.

The green Download button at the bottom of the plot will download the expression data for this feature only across all biosamples.

The Analysis Page

If you navigate back to the analysis page for the expression experiment of interest, you will be able to access both the biosamples and all the expression data loaded for that analysis. The biosample browser will also let you view each biosample loaded for that analsis.

The Gene Search tool is a customized search tool that allows you to find genes, mRNA, etc corresponding to a selected Organism. You can search genes using annotations such as InterProScan and Gene Ontology accessions along with using BLAST hit descriptions. For example, searching for "Endoplasmin homolog" yields the following results.

Downloading Results

Once a search is performed, a Download results as FASTA button becomes available near the top of the page. The results file contains information about each gene, stored in the FASTA header, along with its sequence.

The Basic Local Alignment Search Tool (BLAST) allows you to query all the nucleotide and polypeptide sequences stored in HWG. First pick a query type (nucleotide or protein). You will be able to set search parameters on the next page. Choose the appropriate program based on the Query type and Target database type. Please click on the program name to view the search form.

Once you've selected a BLAST algorithm, you'll be able to paste your query in the box. Next, choose a target organism to search against, and finally, you can set advanced search parameters such as e-value cutoff, word size, and gap/mismatch scoring. Press the green BLAST button at the bottom of the screen when you're ready.

Your page will automatically reload while your job is running: this may take several minutes. The results page will show your search parameters and a table of the results as well as a table of previous BLAST jobs you've run. Click on the blue arrows to the left of each search result to view individual alignments.

When you are satisfied with your search, you can click on the Target name column of the search results to visit the matched feature pages. Alternatively, you can download the full BLAST alignments (html) or the formatted results in XML, GFF3, and tab-delimited format by pressing the green links at the top of the screen. You can also edit and resubmit your job by following the link at the bottom of the screen.

Hardwood Genomics uses Jbrowse to visualize genomes, transcriptomes, and their features. You can reach Jbrowse either through the Jbrowse tool page, or as a field from a feature or organism page.

If you are on a feature (mRNA/mRNA contig) page, clicking on the link will start your Jbrowse session centered on that feature.

Using the Browser

There are many useful Jbrowse guides available online. Some particular tips for using HWG:

• If you would like to go back to a feature's HWG page from the Jbrowse track, right click on it.

• The scaffold dropdown box will only display 30 scaffolds. The rest are still available by typing the scaffold name directly into the box and hitting the Enter button.

• If you are looking for a particular gene of interest, starting from the HWG feature page will let you link directly to it.

• JBrowse can display BLAST results. From the BLASTn tool in HWG, paste in your sequence of interest, select a set of scaffolds as the database and BLAST. When the results are returned, you can click straight through to JBrowse and see the region of identified homology on its own track at the top of the display.

More help

For help using Jbrowse, check out the links below.

• Jbrowse video overview

• Candida Jbrowse guide

• Downloading sequences