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TIBCO Spotfire Lead Discovery, NextGENe, Corona Lite, Velvet, Condensation Tool

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Tibco launched Spotfire Lead Discovery, software that gives researchers a visual and interactive environment for exploring chemical structures and any associated data.
 
The solution allows chemists to access chemistry and biological data in a single analysis environment, then easily build applications for chemical structure analysis, the company said in a release.
 
The solution integrates with cheminformatics software, including Symyx and CambridgeSoft.
 
Spotfire Lead Discovery lets users interact with 3D scatter plots, profile charts, pie charts, bar charts, and histograms, while filtering data via range sliders, check boxes, radio buttons, or search. It can help represent complex data sets and identify relationships between structures, calculated or measured properties, and biological assay results; manage and compare unlimited number of chemical structures; and lets users share analysis, workflow, and decision points.
 

 
Applied Biosystems has announced it is providing new analytical tools for short read de novo assembly of small organisms on the SOLiD 3 System through its SOLiD Software Development Community.
 
One analysis tool from SoftGenetics, called NextGENe, and another from researchers at the European Bioinformatics Institute, Velvet, were developed to help researchers reconstruct, assemble, and visualize short read sequencing data.

 

Velvet, a short read de novo assembly tool developed by the EBI, is an open-source package for assembling short reads into contigs.
 
In collaboration with EBI, ABI developed a de novo assembly bioinformatics pipeline, called Corona Lite, which can produce scaffolds up to 50 kilobases and convert color-space contigs into base space contigs for viewing and analysis.
 
This pipeline provides read quality filters on color-space data, conversion into color-space contigs, and final conversion to nucleotide sequences for consensus calling and error correction, the company said.
 
According to the announcement, ABI and EBI's analysis tools will enable researchers to take data directly from the SOLiD System and produce base-space assemblies.
 
SoftGenetics is a new member of the SOLiD Software Development Community, specializing in the development of genetic analysis tools for both research and diagnostic applications. The company's NextGENe sequencing software helps researchers to analyze data from multiple next-generation sequencing platforms and enables the assembly, alignment, quality control, and annotation of de novo sequencing.
 
Separately, SoftGeneticsannounced that it has added a comprehensive SNP & INDEL viewer to its NextGENe software suite.
 
The suite also contains a so-called Condensation Tool which statistically polishes short reads to increase sequencing accuracy. The new tool developed at the request and in collaboration with researchers whom the company did not name, permits gene annotation and navigation within the genome; offers a view of variations in nucleotides and amino acids; links to NCBI and dbSNP databases; and gives users the ability to view and export consensus sequence providing researchers with an interface for review of the data generated by the next generation sequencing systems.
 
According to the company, Condensation Tool improves sequencing accuracy, identifying and grouping identical anchor sequences followed by elongation of the identical short reads into 50-65 bp fragments.
 
The statistical polishing removes errant base calls and other sequencing anomalies both of which help to increase base call accuracy and variant detection, while the elongation process allows detection of micro indels acrossshort fragments.
 
NextGENe is compatible with outputs from the ABI SOLiD system, Illumina Genome Analyzer, and Roche 454 sequencing technology.

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