Introduction:

To retrieve the data associated with a track in text format, to calculate intersections between tracks, and to retrieve DNA sequence covered by a track, Table Browser is the program for that which we will use for the retrieval and annotation of SARS-CoV-2 Viral Genome. We should know what is genome annotation; Genome Annotation is the process to identify all of the locations of genes and coding regions in a genome.

 

Steps:

Retrieval of the Genome

First go to the Table Browser which you can access from here.

Select the parameters according to the given table for SARS-CoV-2 Genome Retrieval: 

          Parameters                                               Options

          Clade                                                        Viruses

          Genome                                                   SARS-CoV-2

          Assembly                                                  Select the Recent Entry

          Group                                                       Genes and Gene Predictions

          Track                                                         NCBI genes

          Table                                                         ncbiGene

          Region                                                      Genome

          Output Format                                         GTF or BED

          File Type Returned                                   Plain Text

 

NOTE: These chosen options are specifically for SARS-CoV-2 Viral Genome, but you can tweak the choices to get the data based upon your need.

Now click on the ‘Get Output’.

The text file will be downloaded and represented which you can simply analyze.

 

Annotation of the Genome

(A)

The downloaded file can be open on any editor.

For this, first go back to the Table Browser’s parameter page and provide in the ‘Output File’ box, the format name next to the address of your output file.

Type ‘.gtf’ next to your output file and click on the ‘Get Output’.

Drag your downloaded file to the editor e.g. Visual Studio Code.

The Genetic structure of the genome will be displayed on the editor.

You can Annotate the locations of the genes and coding regions of the SARS-CoV-2 Viral Genome.

 

(B)

Same as before, you can go back to Table Browser’s parameter page and change the format type.

This time, select BED (Browser Extensible Data).

In ‘Output File’, next to the file address, add ‘.bed’.

Now click on the ‘Get Output’.

A parameter page will open up, where you have to make sure to select ‘Whole Gene’ option.

Click on the ‘Get BED’ and the BED file will be created.

You can visualize this file just like GTF file.

 

Statistics/Summary of Genes

You must have noticed an option along with ‘Get Output’ on the Table Browser; the ‘Summary/Statistics’ option.

You can select it to get the statistics of your gene data which is a summary of your gene.

 

Summary:

In this video, we learnt about the retrieval of the genome data by taking the example of the retrieval and the annotation of SARS-CoV-2. We got to learn about different annotation files (GFF, GFF3, GTF) and what is the major difference between them.