GENica
 Bioinformatics for Molecular Plant Breeding
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Genome Maps

GENica CMap

Molecular Markers

GENica Marker Tools
  • A prototype database for storing, searching and editing SSR, SNP and DArT® new marker types added: DArT (Sep '07) & SNP (Dec '07) genotype data.
  • The application supports the set-up and analysis of genotyping experiments with Multiplex-ReadyTM markers through online and downloadable applications.
  • To find out more, try the tutorial written August '07, expanded December '07, read the user manual or view screenshots. Contact Gregory Lott to receive a login.
Marker Binner
  • Create groups of microsatellite markers that can be analysed together on a sequencer to reduce genotyping costs.
  • This is the stand-alone version; an integrated version of Marker Binner is available in GENica Marker Tools (see above). Click here for the Marker Binner manual.
  • Login required, contact Gregory Lott to receive a login.

Pedigrees

Ceres Pedigree Viewer
  • A prototype database for searching and viewing pedigrees.
  • Contains ca. 5 million GWIS wheat pedigrees and to ca. 400,000 barley pedigrees, curated by the Plant Improvement Group at the University of Queensland.

Sequence Access and Analysis Tools

BASC ESTDB
  • The public BASC ESTDB gives access to NCBI wheat and barley EST sequences, quality-trimmed and grouped into contigs and clusters. A "Contig view" displays each contig's ESTs, alongside archived BLASTX and BLASTN results for the contig sequence, and a link to the corresponding genome region in Gramene's "Oryza sativa contig viewer".
  • Barley and wheat ESTDB are updated twice a year.
MPBCRC SOE BLAST
  • Perform a BLAST search of general and custom databases for matches to your input nucelotide or protein sequence(s). Results can be directly imported into "Son of Eric" (SOE).
Son of Eric (SOE)
  • SOE allows genome browsing and bioinformatic analyses. It maintains an audit trail of analyses conducted. Use SOE in combination with MPBCRC SOE BLAST to track search results obtained at different times, from different databases, etc.
  • Data can be stored with public access (no login required) or with restricted access. To obtain a restricted access account, contact the CCG.
Multidotter
  • Multidotter is a dot-matrix program that can compare three or more sequences, graphically identifying regions that are conserved between at least two of the sequences. Find out more...
GenBank Batch
  • An easy-to-use web-based interface to retrieve multiple sequences from GenBank.
EMBOSS
  • Access the CCG web installation of EMBOSS to analyse and align nucleotide and protein sequences. For options requiring command line or sequence database access, contact the CCG for advice.
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