Introduce to GC-Profile
    
 
GC-Profile is a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences
 
I Website description
    
 

The web server GC-Profile is implemented on Apache server and the web interface is designed using CGI (Common Gateway Interface) Perl scripts. The segmentation algorithms, which are based on the quadratic divergence and cumulative GC profile, are written in the language of C++. The output graphs are generated by gnuplot graphic routine (http://www.gnuplot.info/).
 
II Inputs and parameters
   
 
GC-Profile has a user-friendly and intuitive input interface. Users can choose to paste the sequence in the box or upload the sequence (FASTA format) in a file.
 

The following inputs are required for the web server GC-Profile.

  1. Halting parameter for segmentation. The default value is 100, but this can be changed according to the requirements of users. Note that halting parameter should be nonnegative.
  2. Minimum length. Generally, the minimum length is set to be 1000 bp for prokaryotic genomes and 3000 bp for eukaryotic genomes.
  3. Gap size to be filtered. The default value is 1% of the input sequence, i.e., gaps more than 1% of the input sequence are retained, otherwise they are simply deleted. Other values are also provided to satisfy user's need.
  4. The graph size to output. It defaults to medium (800*600 pixels). User can change the size from small (640*480 pixels) to giant (2400*1800 pixels).
  5. Whether to label the coordinates of segmentation points to the cumulative GC profile.
  6. Whether to plot z' curve instead of -z' curve. By default -z' curve is plotted.
  7. Whether to set as multiplot mode, in which plots are placed on the same page.
  8. Whether to upload a data file containing density distribution of genes (CpG islands; and other genomic elements). With this option the corresponding distribution will be plotted against the G+C content.
  9. Whether to upload a data file containing absolute coordinates in the input sequence. This option allows users to label the positions of some interesting genes, e.g. horizontally transferred genes, to the cumulative GC profile. It is very useful to reveal the genomic context of these genes.
 
III Outputs
      
 

By default GC-Profile generates four files for each job: two tables and two figures. The output web page shows the process of GC-Profile, and provides links to the results of sequence segmentation: (i) coordinates, sizes and G+C contents of the segmented domains as an HTML table; (ii) number, coordinates, segmentation strength, segmentation times and segmented contig of the segmentation points as an HTML table; (iii) the cumulative GC profile and (iv) the GC content of the input sequence in PNG format. If upload options are chosen, the density distribution or the coordinates points labeled to the cumulative GC profile can also be obtained.