mlstdbNet installation

Required packages

mlstdbNet requires a number of packages to be installed:

Linux packages

• Apache web server
• PostgreSQL database - version 7.2 used in development but any recent version should work fine.
• Perl - version 5.6 used in development.

Perl modules

These are included with most Linux distributions.

• CGI - module to generate and parse dynamic web pages.
• DBI - Database Independent interface - module used to interact with databases.
  • DBD-Pg - PostgreSQL database driver for DBI.
• XML::Parser::perlSAX - part of libxml-perl - Used to parse XML configuration files.

Optional packages

Installing these packages will enable extra functionality, but they are not required.

Third-party programs

• BLAST
• EMBOSS
  • stretcher program - used for sequence alignment in allele query.
  • showalign program - for displaying aligned alleles in the graphical breakdown.
  • fneighbor program - used by Tree plugin for creating UPGMA and NJ trees
• Jalview - Java multiple alignment - used for sequence analysis following allele query (modified version included in download).
• ChartDirector - library used for generating charts.
• ImageMagick - currently used for converting BURST images to PNG format. Required for BURST plugin.

Perl modules

• BioPerl
  • Bio::AlignIO - used to generate allele sequence files in different formats for download.
  • Bio::Biblio::IO - used to parse XML files from PubMed.
• Mail::Sender - used to send exported datasets by E-mail.
• Compress::Zlib - used to compress exported datasets.
• LWP - Library for WWW access - used to download PubMed citations.