Welcome to the Severe Acute Respiratory Syndrome Coronavirus (SARS CoV) resource help page. This resource was developed to provide data and information relevant to SARS CoV. It includes links to the most recent sequence data and publications, to other SARS related resources, and a pre-computed alignment of genome sequences from various isolates.

Genome tool overview

The genome tool is comprised of two panels: The upper panel gives an overview of the entire SARS CoV genome and allows quick navigation to specific regions of the genome. The lower panel displays an alignment of all full-length SARS Coronavirus genomes present in GenBank as of July 1, 2009. The nucleotide sequences displayed were aligned using Muscle v3.7.

Genome tool help contents

Navigation
Sequence variation
Genome features
Search box
Magnification controls
Genome features
Anchor sequence
Sequence alignment

Top panel

There are five basic features to the top panel of the genome viewer, a ruler to indicate nucleotide position along the SAR CoV genome, a navigation slider, a variation histogram, a features diagram, and a search box.

Navigation

When the viewer loads, the navigation slider is located in the upper left hand corner of the top panel. To move along the SARS CoV genome, place the mouse over the rectangular, colored slider handle, press and hold the left mouse button, and move the slider left or right within the panel. When the mouse button is released, the sequences displayed in the lower panel will adjust to the new position. The exact position of the slider is denoted in the upper left hand corner on the top panel, 'Region displayed.'

Sequence variation

A frequency based algorithm is used to calculate variations among the genome sequences included in the alignment. These sequence differences are plotted in red in the histogram. Variations in sequence coverage between genomes in the alignment are plotted in blue. These variations typically represent incomplete sequence information at the viral ends.

Genome features

The SARS CoV coding sequence features (CDS features) are depicted as green rectangles in the top panel. These CDS features include viral proteins (and polyproteins) and are mapped in their correct positions along the viral genome.

Search box

A search box is located in the upper right hand corner of the top panel. Searches can include any term found within the GenBank records present in the alignment, such as accession number, strain identifier, author, or geographic location. All records containing a queried search string are displayed in a new window, and an individual record can be selected from the list.

Bottom panel

The bottom panel displays the aligned SARS CoV nucleotide sequences and includes five basic elements, magnification controls, nucleotide sequences listed by accession number, alignment anchor sequence, and variation histogram.

Magnification controls

In the upper left hand corner of the bottom panel are three magnification controls, a zoom in button (+), a zoom out button (-), and a zoom to sequence button (ATG). These are operated by moving the mouse cursor over the control and depressing the left mouse button. Any changes to the zoom level with the bottom panel are reflected in the navigation slider in the upper panel.

Nucleotide records

All of nucleotide records used in the alignment are listed by accession number along the left hand side of the bottom panel. Next to each accession number there is a green arrow pointing at a box. If this box contains a '+,' then this entry can be 'expanded' and the CDS features visualized under the associated nucleotide sequence.

The name of a particular accession can be seen by placing the mouse cursor over the accession number (or sequence), clicking the left mouse button. The GenBank record of that accession can be seen by placing the mouse cursor over the sequence (or accession number), clicking the left mouse button, and selecting that accession number from the menu.

Anchor sequence

The anchor sequence for the alignment and the associated accession number are located above the rest of the alignment in the top portion of the bottom panel. When the viewer initially loads, the RefSeq genome of SARS CoV is positioned as the anchor sequence. The rest of the aligned sequences are ordered in reference to this sequence.

The anchor sequence can be changed to the alignment consensus by placing the mouse cursor over the anchor sequence (or anchor accession number), clicking the left mouse button, and selecting 'Reset consensus as anchor.' Any sequence in the alignment can be selected as the anchor sequence by placing the mouse cursor over the sequence (or accession number), clicking the left mouse button, and selecting that accession number 'as anchor.' Any changes to the anchor sequence are reflected in the sequence variation histograms.

Sequence alignment

The sequence alignment is shown below the anchor sequence. It can be visualized in two ways: All nucleotides in each sequence can be shown, or only those nucleotides that differ from the consensus can be shown. Initially, all nucleotides are shown, but this can be changed by placing the mouse cursor over any sequence (or accession number), clicking the right mouse button, and selecting or deselecting 'use dots.'

Differences between a given sequence and the anchor sequence are highlighted in red or blue. A red block over a single nucleotide indicates that this nucleotide differs from the anchor sequence at the same position. Blue over- and under-lines indicate that the marked sequence includes an insertion compared to the anchor sequence. To see the inserted sequences, select the marked sequence as anchor. A bold red line in place of sequence indicates a deletion relative to the anchor sequence.