Demonstration
Below is an example of the GenomeBlast options page. A user can define parameters based on queries to be compared. Here, "Low Complexity" and "Mask for Lookup Table Only" have been left unchecked. Default values for Expect and Wordsize have remained at 10 and 3, respectively. Default matrix, Blosum62, has been selected, along with default Gap Cost.
Upload Genome Sequence Files:
A user can enter the number of files to be uploaded, and the specified number of files can be uploaded individually.
Blastp Parameters:
Coverage and Identity parameters should be defined on this page. Default values have been chosen. The Expect Value may be changed, although we recommend altering coverage and identity first to produce desired output.
Results:
The top of the results page displays what parameters from the previous window have been selected, and all genomes that were compared. If needed, parameters can be modified without perfoming pairwise comparisons. Also displayed is a description of the three classifications of genes found in the comparison.
Unique Genes:
To display unique genes found by comparison of genomes, a user can select which genomes to include. One or all genomes may be selected. Note: two separate windows are shown.
Homologous Genes:
Homologous genes may be viewed in the same manner as unique genes; simply click which genomes are to be included. Note: two separate windows are shown.
Pairwise Genome Comparison:
A visual representation of a pairwise genome compairson is available. This can be viewed by either clicking on the genome pairs name above the preview plot, or by selecting genome pairs from the drop down menu. Once the pairwise genome compairson is displayed, dots/lines will be shown representing the % identity, correspondingn to each of the four given colors. Users can display the query, subject, and identity for specific dots within each plot by clicking on the desired dot.
All Genome Comparison:
Several All-Genome Comparisons are available in addition to pairwise genome compairsons.
Phylogenetic Tree:
A phylogenetic tree is also available. It displays the most parsimonious tree unrooted in a "branch and bound" representation.
Gene Presence / Absence:
Gene Presence / Absence Table is available. It displays the presence or absence of 10 genes at a time in each table, and describes whether the gene is unique, homologous or other in terms of all genomes compared.
Gene Summary Table:
The Gene Summary Table is similar to the Gene Presence / Absence Table, but provides more detailed information as to which specific gene is present in each genome. In addition, the gene is also identified as homologous, unique, or other.
