VibrioBase: A Model for Next-Generation Genome and Annotation Database Development

Figure 1

A workflow of the PGC tool. Through an input web interface on VibrioBase, users can choose two genomes of interest (reference versus query genomes) in VibrioBase and parameters for comparison. Three available useful parameters/thresholds which are the minimum percent identity, merge threshold, and link threshold. The minimum percent identity parameter will display aligned genomic regions (represented by colored links) once the sequence identity is higher than the user-defined cut-off. Similar to the merge threshold, this threshold will merge two links if the distance between the two regions is lower than the user-defined cut-off. The link threshold ignores links in the diagram if their widths are lower than the user-defined cut-off. Once the job is submitted to our server, PGC pipeline parses this information and starts the genome alignment with NUCmer. A series of in-house Perl and Python scripts are used to parse the NUCmer output and generate different text files: (1) Karyotype.txt stores information about the contigs and their colors used in Circos; (2) Links.txt stores information about the aligned genomic regions; (3) Band_labels.txt keeps the names of each contigs/chromosome. The Circos.conf configuration file will be created using the information in the above four files, which is needed for displaying the two aligned genomes with Circos.