User Manual

Follow these steps to use the web application...

• Step 1: Upload your files
• Step 2: Configure parameters
• Step 3: Click submit

Input files format

• Gene-family Data File*: A file (.xlsx/.csv/.tsv) containing gene family and location information for each gene that must maintain the structure as follows:

  gene_id	gene_family	chromosome	start	end	strand
  gene_1	family_1	chr_1	4031	15104	-
  gene_2	family_2	chr_2	24310	45159	+
  ...	...	...	...	...	...
  centro_1	centromere	chr_1	82125	98476	0

  The naming convention for the header row must be followed strictly. Centromere data is optional and it is required only when you want to plot them. If you want to plot the centromeres along with genes belonging to different gene-families, always put centromere under gene_family and 0 under strand columns. For example, see test data 1, test data 2, or test data 3.
• Genome or Chromosome-Lengths File*: A fasta (.fasta/.fna/.fa) file containing the genome sequence or a text (.txt) file containing the chromosome ids with their lengths; seq_id,seq_length per line:

                  
                      >chr_1
                      ACGT........
                      >chr_2
                      ACGT........
                      >...
                      ............
                  
              

  For example, see sample fasta file.

                  
                      chr_1,length_of_chr_1
                      chr_2,length_of_chr_2
                      ...
                  
              

  For example, see sample chromosome-lengths file.
• Color Map File: A text (.txt) file contating the gene family (gf) ids with their color codes; gf_id,color_code or gf_id,[0,1],[0,1],[0,1] per line (RGB values). If assigning colors based on provided color code, structure the color map file as follows:

                  
                      gf_1,1
                      gf_2,2
                      ...
                  
              

  This will assign red to gf_1, green to gf_2 and so on. For example, see sample color file. For color assignment of gene-families using the provided color code, refer to the following palette:
  
  If assigning colors based on your own choice, provide the corresponding RGB values for each gene family as follows:

                  
                      gf_1,0.x,0.y,0.z
                      gf_2,0.i,0.j,0.k
                      ...
                  
              

  For example, see custom color file.

Limitations

At present, GFViewer can handle plotting a maximum of 19 different gene-families with the default color palette where color code: 20 (grey) is reserved for centromeres.

Free Access Statement

GFViewer is provided free of charge to all users, including both academic and commercial users. We encourage everyone to utilize this tool to advance research, development, and commercial endeavors in their respective fields. No additional permissions or licenses are required for commercial use. Please ensure proper citation of GFViewer in any publications, presentations, or projects derived from its use.