# Metadata-driven Comparative Analysis Tool (meta-CATS)

*Revised: February 22, 2024*

## Overview
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.  

## See also
* [Metadata-driven Comparative Analysis Tool (meta-CATS)](https://bv-brc.org/app/MetaCATS)
* [Metadata-driven Comparative Analysis Tool (meta-CATS) Tutorial](/tutorial/metacats/metacats)

## 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](../images/bv_services_menu.png) 

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

![Figure 1](../images/metacats_Picture1.png "Figure 1") 

## Parameters

**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.

## Buttons

![Figure 2](../images/metacats_Picture2.png "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](../images/metacats_Picture3.png "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](../images/metacats_Picture4.png "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](../images/metacats_Picture5.png "Figure 5")

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

![Figure 6](../images/metacats_Picture6.png "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_references/action_bar) Quick Reference Guide.