About

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.

Reference

Grant JR, Stothard P (2008) The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res 36:W181-W184.

Required settings

Email address

Enter your email address Help

Your results will be emailed to the address you provide.

Primary genome sequence

Upload a DNA sequence Help

The CGView Server can draw maps of plasmid, mitochondrial, chloroplast, or bacterial DNA sequences. The sequence should be in GenBank, EMBL, FASTA, or raw format, and should be at least 1000 bases long.

Optional settings

Upload a GFF file describing gene or COG information Help

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.

Example:

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 Help

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.

Example:

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: bp Help

    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: bp Help

    Overlaps can be added to the query subsequences to ensure that similarity blocks aren't missed or truncated in the vicinity of query splits.

BLAST 1

  • BLAST program: Help
    • blastn: DNA vs. DNA BLAST
    • tblastx: translated DNA vs. translated DNA BLAST
    • blastx: translated DNA vs. protein BLAST

    Note that conserved DNA sequences can produce tblastx hits in all six reading frames, even when many stop codons are present.

  • Expect value cutoff: Help

    The number of matches expected by chance. Lower expect values are more stringent.

  • Filter low complexity sequences Help

    Whether to filter low complexity sequences out of the query sequence.

  • Genetic code: Help

    The genetic code to use for translated BLAST searches.

  • Alignment length cutoff: Help

    The minimum acceptable alignment length for BLAST hits. BLAST hits with an alignment length lower than this value will be ignored. This value must be greater than or equal to 10. If no value is given then all BLAST hits are kept.

  • Percent identity cutoff: % Help

    The minimum acceptable percent identity for BLAST hits. BLAST hits with a percent identity lower than this value will be ignored. This value must be between 1 and 100. If no value is given then all BLAST hits are kept.

  • BLAST program:
  • Expect value cutoff:
  • Filter low complexity sequences
  • Genetic code:
  • Alignment length cutoff:
  • Percent identity cutoff: %
  • BLAST program:
  • Expect value cutoff:
  • Filter low complexity sequences
  • Genetic code:
  • Alignment length cutoff:
  • Percent identity cutoff: %

Output settings

  • Map title . Help

    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. Help

    Whether features read from GenBank or EMBL files should be drawn.

  • Show GC content. Help

    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. Help

    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 . Help
    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. Help

    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: Help

    Specify which codons qualify as start and stop codons. These settings also affect ORF identification.

    • Start:
    • Stop:
  • Show blast hits by reading frame. Help

    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).

  • Show labels. Help

    Whether feature labels should be shown.

  • Show legends. Help

    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. Help

    The font size to use for feature labels. Smaller fonts allow more labels to fit on the map.

  • Show a view of the chromosome. Center zoomed maps on base , and expand the region times. Help

    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.

  • Tick density . Help

    The density of the tick marks on the map. Smaller values produce fewer tick marks.

  • Draw features as . Help
    arrow and arc
  • Show divider rings. Help

    Whether complete rings should be drawn between feature slots, to better separate results.

  • Use opacity for BLAST hits. Help

    Whether BLAST hits should be drawn with partial opacity, so that overlapping hits can be visualized.