BacMap: An Interactive

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BacMap An Interactive Picture Atlas for
Exploring Bacterial Genomes
Lab Presentation Paul Stothard stothard_at_ualberta.c
a 2005-02-04
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Reasons for Creating BacMap

• Graphical maps of DNA sequence features provide
  a means to quickly view the characteristics of
  specific genomic regions or genes.
• Maps can be used to identify candidate operons
  in bacterial species.
• Maps of different species can be compared to
  identify evolutionarily conserved gene order.
• Genes can be linked to detailed textual
  annotations.

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Existing Solutions
NCBIs bacterial genome browser
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Existing Solutions
NCBI bacterial genome browser

• Difficult to navigate because only two zoom
  levels are provided.
• Map switches between circular and linear view.
• Gene labels often not shown because of space
  restrictions.
• Cannot move map to region of interest using text
  search or sequence search.

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Existing Solutions
TIGR comprehensive microbial resource
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Existing Solutions
TIGR comprehensive microbial resource

• Difficult to navigate because only two zoom
  levels are provided.
• Map switches between circular and linear view.
• Cannot move map to region of interest using text
  search or sequence search.

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CGView
Circular Genome Viewer
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CGView

• Java application and library for generating high
  quality, zoomable maps of circular genomes.
• Converts XML or tab delimited input into a
  graphical map (PNG, JPG, or Scalable Vector
  Graphics format).
• Supports labels, legends, and footnotes.
• Zooming relies on standard hyperlinks rather
  than browser plug-ins.

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Software Used by BacMap

• CGView genome maps, maps for BLAST and text
  search results.
• BacMapGraph sequence statistics graphs.
• BASyS automated annotation of gene sequences.
• BLAST sequence similarity searching.
• Glimpse text searching.
• BioPerl parsing feature information from
  GenBank files, parsing BLAST results.
• Custom Perl modules creating data files for
  the various programs, obtaining genome data from
  NCBI.
• Custom Perl scripts building the BacMap web
  site while logging errors. Processing BLAST and
  text searches.

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Organization of BacMap
BacMap
docs
lib
Perl scripts and modules
NCBI data
processed data
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Filling the BacMap Database

• Download new genomes from NCBI.
• Create species cards.
• Create genome cards.
• Apply patch file to fix problems.
• Create gene cards.
• Format databases for BLAST.
• Create index files from gene cards for text
  search.
• Create XML input for CGView.
• Create hyperlinked CGView maps.
• Create sequence statistics graphs.
• Import gene cards from BASyS.

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Handling Configuration Issues

• BacMap code avoids hard-coded file paths.
• All path information is stored in a file called
  bacmap.conf.
• A BacMap Perl module is used to obtain
  information from the bacmap.conf file
• use BacMapUtilGetConfInfo
• my conf new BacMapUtilGetConfInfo()
• my pathToJava conf-gtgetPath(java)

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Handling Errors

• BacMap uses Error.pm to provide try, throw, and
  catch capabilities
• use Error
• try
• makeDir()
• catch Error with
• my ex shift
• print ex-gt'-text' . "\n"
• print ex-gt'-stacktrace' . "\n"
• other error handling code
• sub makeDir mkdir (somePath, 0775) or throw
  ErrorSimple("Could not create somePath dir.")

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Logging Update Progress and Errors

• A BacMap Perl module is used to write update
  progress and error information to a log.txt file
• use BacMapUtilLogManager
• my log new BacMapUtilLogManager()
• log-gtlogNotice("Updating CGView linked maps.")

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Accessing BacMap
http//wishart.biology.ualberta.ca/BacMap/
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Species Information
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Genome Maps
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Gene Annotations
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Text Search
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BLAST Search
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Sequence Statistics
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Downloads
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Version 2

• Relational database instead of flat files.
• Support for more complex text queries.
• Web interface for managing the site.