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Ingenuity Analysis Services, GeneDirectory V2.01, NextGENe, Scaffold 2.1

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Ingenuity Systems said this week that it has begun offering custom-tailored professional services for scientists working with omics data related to compound profiling, target identification, and mechanism-of-action studies.
 
The offering, called Ingenuity Analysis Services, is designed to meet the needs of research teams seeking a rapid turnaround or who do not have the required resources internally, the company said.
 
Examples of Ingenuity Analysis Services offerings include analysis and interpretation of omics datasets for compound profiling, lead identification, and prioritization of therapeutic targets, and understanding disease mechanism of action and mechanism of toxicity; building biological models of disease processes for target identification and validation research; identification and prioritization of biomarkers via analysis of gene expression array, proteomics, or genotyping data; delivering toxicity and safety assessment of drug candidates; and creating report summaries and graphics or pathways for presentations or publications.
 

 
Syngene has launched GeneDirectory V2.01, its upgraded software package for automated gel data storage and analysis. It has new features that the company said will allow easier use in genetic fingerprinting studies, cluster analysis, analysis of variable number of tandem repeats, analysis of restriction fragment length polymorphisms, and genotyping.
 
GeneDirectory is equipped with bootstrapping, a random statistical re-sampling technique. Using bootstrapping, GeneDirectory automatically selects bands and re-samples them many times so matching patterns can be assessed for the validity of their matching, the company said in an announcement. The resultant bootstrapping values are displayed alongside the dendrograms.
 
The software lets users view long tracks and permits unlimited elements in a composite track to be used for band matching. The tracks can be analyzed by cluster analysis, profile matching, and band matching via a pattern of bands or an entire profile. The resulting data, aligned dendrograms and aligned track images can also be automatically exported to Excel.
 

 
State College, Penn.-based SoftGenetics has added a conversion tool to its NextGENe software suite for “color space,” or CS Fasta files, generated by the ABI SOLiD sequencing system. The new tool converts and corrects “color space” data into “base space” data to enable de novo assembly, target assembly, SNP/indel detection, transcriptome, and other analysis with NextGENe.
 
The conversion tool works simultaneously in color space and base space, comparing and correcting obvious errors to maximize the inherent accuracy of the SOLiD system, the company said.
 
In the SOLiD system each color call is predicated on the prior call, which the company said can propagate errors that occur in the translation from color space to base space. The NextGENe conversion tool can correct the errant call, thus eliminating the error propagation, the company said.
 

 
Agilent Technologies and Proteome Software said this week that Proteome's Scaffold 2.1 software now supports search results processing by Agilent's Spectrum Mill protein database search engine.
 
Scaffold 2.1 statistically validates peptides and proteins from tandem mass spectrometry data, combines results from multiple search engines, and graphically displays identifications in biologically relevant formats, the companies said. Spectrum Mill performs high-throughput protein database searches of MS and MS/MS data.
 
Researchers who load Spectrum Mill data files into Scaffold can now compare Spectrum Mill results with those of the Mascot, Sequest, Phenyx, OMSSA, and X! Tandem search engines.
 
Scaffold 2.1 can be found here.

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