Metadata-driven Comparative Analysis Tool (meta-CATS)


The meta-CATS metadata genome comparison tool takes sequence data and determines the aligned positions that significantly differ between two (or more) user-specified groups. Once an analysis is started, a multiple sequence alignment is performed if the input was unaligned (such as from a database query). A chi-square test of independence is then performed on each non-conserved column of the alignment, to identify those that have a non-random distribution of bases. A quantitative statistical value of variation is computed for all positions. Columns that are perfectly conserved will not be identified as statistically significant. All other non-conserved columns will be evaluated to determine whether the p-value is lower than the specified threshold value. Terminal gaps flanking the aligned sequences will not be taken into account for the analysis.

Using the Meta-CATS Service

The Meta-CATS submenu option under the “SERVICES” main menu (Viral Services category) opens the Meta-CATS Service input form. Note: You must be logged into BV-BRC to use this service.

Meta-CATS menu option


Below is a screenshot of the Meta-CATS landing page, as well as a summary of customizable parameters.

Figure 1

P-value: the probability of the observed data given that the null hypothesis is true.

Output Folder: The workspace folder where results will be placed.

Output Name: A user-specified label. This name will appear in the workspace when the analysis job is complete.

Fasta Text Input: Users may enter custom sequences here by pasting in FASTA formatted sequences.

Input Options

Auto Grouping: Allows users to group sequences by available metadata such as: host, country, year, virus type, host age, host gender, etc. The appropriate metadata field may be selected from the “METADATA” drop-down menu.

And/or Select Feature Group: Users may input a nucleic acid or protein FASTA file containing a previously selected “Feature Group” (eg. CDS, tRNA etc.) from their workspace here, either in addition to the FASTA text input, or as an alternative.

Metadata: Auto grouping by available metadata options includes: Host name, geographic location, isolation country, species, genus, and collection year.

Feature Groups: This option allows users to select previously identified groups of sequences saved to their workspace.

Alignment File: This option allows users to select a previously aligned group of nucleotides or proteins.

Select Feature Group: This option allows users to specify feature groups previously saved to their workbench.

DNA/PROTEIN: Allows users to specify whether their sequences are nucleic acid or protein sequences.

Group names: User-specified names for custom groups.

Delete Rows: Allows users to delete unwanted sequences.


Figure 2

Reset: Resets the input form to default values

Submit: Launches the MSA job. A message will appear below the box to indicate that the job is now in the queue.

Figure 3

Output Results

Clicking on the Jobs indicator at the bottom of the BV-BRC page open the Jobs Status page that displays all current and previous service jobs and their status.

Figure 4

Once the job has completed, selecting the job by clicking on it and clicking the “View” button on the green vertical Action Bar on the right-hand side of the page displays the results files (red box).

Figure 5

The results page will consist of a header describing the job and a list of output files, as shown below.

Figure 6

The Meta-CATS Service generates several files that are deposited in the Private Workspace in the designated Output Folder. These include:

  • chisqTable.tsv - a tab separated value file with results for a “Chi-square Goodness” of fit test result: ie: positions that have significant non-random distribution between the specified groups

  • mcTable.tsv - a tab separated value file with results for adjusted p-values for multiple comparisons.

  • Mafft.log - an output log file produced by the Mafft aligner.

Action buttons

After selecting one of the output files by clicking it, a set of options becomes available in the vertical green Action Bar on the right side of the table. These include:

  • Hide/Show: Toggles (hides) the right-hand side Details Pane.

  • Guide Link: to the corresponding Quick Reference.

  • Download: Downloads the selected item.

  • View: Displays the content of the file, typically as plain text or rendered html, depending on filetype.

  • Delete: Deletes the file.

  • Rename: Allows renaming of the file.

  • Copy: Copies the selected items to the clipboard.

  • Move: Allows moving of the file to another folder.

More details are available in the Action Bar Quick Reference Guide.