The CGView Server is a comparative genomics tool for circular genomes (plasmid, bacterial, mitochondrial, and chloroplast) that allows sequence feature information to be visualized in the context of sequence analysis results. A genome sequence is supplied to the program in FASTA, GenBank, EMBL, or raw format. Up to three comparison sequences (or sequence sets) in FASTA format can also be submitted. The CGView Server uses BLAST to compare the genome sequence to the comparison sequences, and then converts the results and any available feature information (from the GenBank, EMBL, or optional GFF file) or analysis information (from an optional GFF file) into a high-quality graphical map showing the entire genome sequence, or a zoomed view of a region of interest. Several options are available for specifying how the BLAST comparisons are conducted, and for controlling how results are displayed. To see what the CGView Server is capable of, see the examples page.
Grant JR, Stothard P (2008) The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res 36:W181-W184.
Primary genome sequence
Upload a GFF file describing gene or COG information
You can provide a GFF (General Feature Format) file describing sequence features that you would like to visualize. The file should contain tab-separated or comma-separated values, and should have the following column titles, in the following order: 'seqname', 'source', 'feature', 'start', 'end', 'score', 'strand', and 'frame'. The first line in the file you supply must be the column titles. For a given entry, 'seqname' should be the name of the gene, 'feature' should be the type of gene ('CDS', 'rRNA', 'tRNA', 'other') or the single letter COG category ('J' for example). 'start' and 'end' should be integers between 1 and the length of the sequence, and the 'start' value should be less than or equal to the 'end' regardless of the 'strand' value. The 'strand' value should be '+' for the forward strand and '-' for the reverse strand. All other values can be given as '.' or left blank, since they are ignored.
seqname source feature start end score strand frame
GENE1 EMBL CDS 103 1500 . + .
GENE2 EMBL CDS 2400 3623 . + .
GENE2 EMBL tRNA 1600 1700 . + .
Upload a GFF file describing analysis results
You can provide a GFF (General Feature Format) file describing analysis results that you would like to visualize. The file should contain tab-separated or comma-separated values, and should have the following column titles, in the following order: 'seqname', 'source', 'feature', 'start', 'end', 'score', 'strand', and 'frame'. The first line in the file you supply must be the column titles. Only the 'start', 'end', and 'score' values are required--the other values can be left blank or given as '.'. 'start' and 'end' should be integers between 1 and the length of the sequence, and the 'start' value should be less than or equal to the 'end' regardless of the 'strand' value. The 'score' value should be a real number, positive or negative.
seqname source feature start end score strand frame
. . . 103 1500 0.53 . .
. . 1500 1600 0 . .
. . . 2400 3623 -0.25 . .
Upload up to three DNA or protein sequence files in FASTA format for BLAST comparison. Each file can contain one or more sequences:
Global BLAST settings:
- Query split size:
This setting determines the size of the query segments (obtained from the primary genome sequence) used in the BLAST search. This setting can be adjusted if there is concern that a particular similarity block might be truncated due to the location of query splits.
- Query split overlap size:
Overlaps can be added to the query subsequences to ensure that similarity blocks aren't missed or truncated in the vicinity of query splits.
Map title .
A title for the sequence, to appear on the map. If a title is not specified, a title will be obtained from the input sequence file (for FASTA, GenBank, and EMBL input).
Show GenBank/EMBL features.
Whether features read from GenBank or EMBL files should be drawn.
Show GC content.
Whether GC content should be drawn. The GC content is plotted using a sliding window, as the deviation from the average GC content of the entire sequence.
Show GC skew.
Whether GC skew should be drawn. GC Skew is calculated using a sliding window, as (G - C) / (G + C). The value is plotted as the deviation from the average GC skew of the entire sequence. The origin of replication is often associated with a change in sign of the GC skew.
Show ORFs larger than
codons and display them
Whether open reading frames (ORFs) should be drawn. ORF cutoff size must be greater than or equal to 30 codons. The start and stop codons used during ORF identification can be specified below.
- Combined: draw ORFs with each strand (+ and -) represented by a separate ring.
- Separated: draw ORFs with each reading frame (1, 2, 3, -1, -2, -3) represented by a separate ring.
Show start and stop codons.
Whether the positions of start and stop codons should be drawn. By default a start codon is defined as ATG and stop codons are defined as TAA, TAG, and TGA. These settings can be changed below.
- Start and stop codons:
Specify which codons qualify as start and stop codons. These settings also affect ORF identification.
Show blast hits by reading frame.
Whether BLAST results should be split into separate feature rings on the map, based on query strand and reading frame (for tblastx and blastx searches).
Whether feature labels should be shown.
Whether a feature legend and information legend (giving sequence length and accession) should be added to the map.
Use a font size of
for feature labels.
The font size to use for feature labels. Smaller fonts allow more labels to fit on the map.
view of the chromosome. Center zoomed maps on base
, and expand the region
A map showing the entire sequence can be drawn (full), or an expanded view showing more detail for a smaller portion of the map can be drawn (zoomed). When a zoomed map is drawn the map canvas is centered on a specific base in the sequence.
The density of the tick marks on the map. Smaller values produce fewer tick marks.
Draw features as
Show divider rings.
Whether complete rings should be drawn between feature slots, to better separate results.
Use opacity for BLAST hits.
Whether BLAST hits should be drawn with partial opacity, so that overlapping hits can be visualized.