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Old 11-23-2010, 01:29 PM   #1
Geneious
Registered Vendor
 
Location: New Zealand

Join Date: Jul 2010
Posts: 22
Default Geneious Pro 5.3 Beta available now!

Geneious Pro™ continues to improve, with the beta of version 5.3 available now. Download Geneious Pro 5.3 Beta to get a sneak peak at the latest features and send us your feedback. As usual, you can also continue to request features you'd like to see in future versions on our userforums.

The improvements in Geneious Po 5.3 Beta include:
  • Compatibility with Geneious Server™ full release (enquire here)
  • Fine-tune any imported reference assemblies
  • Reduced memory usage when importing large contigs, and alignments
  • Separate raw paired 454 data by linker sequence
  • Separate multiplex sequences by barcode
  • Multi-threaded BLAST for faster sequence searching
  • GFF 3.0 import and handling
  • Print phylogenetic trees across multiple pages
  • Export .ACE files
  • FramePlot functionality for GC prediction
  • Chromatogram trace resizing
  • For a full list of features in Geneious Pro 5.3 see the features page

Virus Hunters Beta Test Geneious Server
Dr. Charles Chiu, MD/PhD, and the viral discovery research team at the University of California, San Francisco (UCSF) are a Geneious Server private beta partner.

Dr. Chiu's work originated in the laboratories of Drs. Joseph DeRisi, PhD and Don Ganem, MD, known for their invention of the Virochip microarray which made a key contribution to the identification of the SARS coronavirus. When electron microscopy was unable to conclusively identify the SARS coronavirus, the Virochip, containing thousands of probes derived from the sequences of all known viruses, identified this novel virus within 24 hours.

Dr. Chiu's team specializes in discovering unidentified or novel viruses associated with both acute and chronic human diseases. In addition to microarrays, the use of next-generation deep sequencing technologies allows rapid, high-throughput screening. State health agencies and researchers worldwide regularly send samples from suspected viral outbreaks to Dr. Chiu’s lab for identification.

On average, the team identifies one new virus every year. One such virus is a novel adenovirus identified during a recent outbreak of Titi monkeys at UC Davis. The virus, a member of an entirely new group of adenoviruses, was the cause of a severe pneumonia outbreak among infected monkeys with an 83% case-fatality rate. Furthermore, seroprevalence studies suggest that a scientist working at the center was also infected by the new adenovirus.

The team is currently using the multi-threaded Geneious Assembler™ on Geneious Server to fully utilize the multiple processors in their 16-core, 96 GB RAM server computer. Samples are analyzed by Illumina next-generation sequencing, with 30 – 100 million sequence reads generated per sample initially aligned to known sequences in the GenBank nucleotide database (containing human, bacterial, viral, and other sequences). The leftover reads are seamlessly offloaded to the Geneious Server and assembled de novo. The Geneious Assembler out-performed all other assemblers tested for in the lab's viral metagenomics workflow using a set of 17 samples from the 2009 H1N1 influenza outbreak.
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