Download Title: GeneWiz browser: An Interactive Tool for Visualizing

Title: GeneWiz browser: An Interactive Tool for
Visualizing Sequenced Chromosomes
By
Peter F. Hallin, Hans-Henrik Stærfeldt, Eva Rotenberg, Tim T.
Binnewies, Craig J. Benham, and David W. Ussery
Published on Standards in Genomic Sciences (2009) 1: 204-215
Citation count: 35
Background
• Over 15 years of the genomic sequencing development, the
public genome database has held more than a thousand
sequenced genomes.
• It is explicitly useful for biologists to analyzed multiple genomes
cross different species for a broad range of interests,
especially:
o identify the phylogenetic relationship, genomic region causing the
pathogencity to human and animals
o new targeted genes worthy for industrial and economical use.
• Such availability of the analytics tools is limited and often
requires users with both analytical and programming
knowledge, hence the analysis of multiple genomes is not
always easy in a broad range of the biological research.
Function of the GeneWiz browser
• GeneWiz browser for visualizing genomic data of prokaryotic
chromosomes.
• This tool provides several functions:
o visualizing whole genome homology of genes and proteins within a
reference strain compared to other strains or species
o visualizing DNA physical properties such as curvature along the
chromosome
o identifying the repeat sequences along the chromosome
o Additionally, custom numerical data such as gene expression and
regulation data can also plotted
• This web-interface service provides an interoperable method
to carry out whole genome visualization
Implementation of GeneWiz browser
• The method behind this visualization tool is to convert
numerical information to color-encoded lanes in either using a
linear scale with a fixed minimum and maximum range, or a
dynamic scale of standard deviations.
o DNA properties based on various developed methods to indicate
particular regions posing biological functions
o Mapping of homologous genes by BLAST (Basic Local Alignment Search
Tool)
o Mapping of short sequencing reads with the weighted coverage
o Custom lanes with pre-processed data provided by users
Workflow of GeneWiz browser
• This web interface includes two parts:
1. the client is written as a JavaApplet that obtains the data remotely from
the server
2. the server is written in Perl/CGI, while a compiled C-program handles the
access to the binary data files.
• All input/output objects are defined in a separated XSD file
(XML schema definition) within the WSDL file,
• MySQL on the server provides the storage function for prebinning of data for each zoom level
• The maximum uniqueness quality is shown for the actual reads
(green-to-blue lane) plotted along with reference genome.
• This figure shows that a good correspondence between the
in-silico and experimental reads suggests little bias towards
certain chromosomal regions if read coverage is around 40
times.
• BLAST comparison of 14 closely related bacteria chromosomes.
• This figure clearly indicates that a strong preference of
deletion on the pathogenic islands exist for a few of bacteria
not causing infection to human.
• A final example illustrates how the marks indicating the
uniqueness of DNA physical properties can be used to
integrate known regulatory elements and gene annotations to
draw a more complete picture of a particular region for gene
expressions.
Summary
•
•
Most biologists believe that a visualization of the multidimensional
genomic information is necessary, but the use of an analytic tool
is relatively difficult to them.
GeneWiz browser is superior to numerous tools which are all the
command-line programs generating publication quality static
images and vector graphics for the genomic visualization.
o easily navigate using mouse
o zooming function to allow users to interpret the genomic information at varying
scales
o an automatic workflow that can be directly called from the users via the client
part
• This tool can be relevant in many pangenomic (crosssequenced-species) as well as in metagenomic (crossunsequenced-species) studies, by giving a quick overview of
clusters of insertion sites, genomic islands and overall
homology between a reference sequence and a data set.