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The company says that the server provides flexible options for executing centralized services, easy integration with other applications and services, powerful database communication and data integration, and a secure access control framework and central-action logging. CLC Bio describes the Genomics Server a bioinformatics solution built on a three-tier server architecture. “A key to our success is that our customers can mix data, and that will continue with new platforms,” he says.Įarly in 2010, the company released version 2.0 of the CLC Genomics Server, an enterprise platform for next-generation sequencing data analysis.

Clc sequence viewer help software#

This overlying strategy extends to software in development to handle the hundreds of thousands of reads generated by upcoming third-generation sequencers. Because different sequencing instruments offer different advantages, it makes sense to mix datasets into hybrid assemblies, Knudsen notes. Users of CLC Bio’s software are not locked into a single platform, but can use any or all HTS machines. “We had a head start in the market, making us a premiere solution provider.” When first launched, “no other companies were doing this,” says Knudsen. The CLC Genomics Workbench is a comprehensive package that analyzes and visualizes data from all major next-generation HTS platforms, such as SOLiD by Applied Biosystems, 454 GSflx by Roche, and Solexa by Illumina. “So there’s a critical demand for solutions that are really adept at handling and analyzing these huge amounts of data,” he says. In fact, the amount of genomic sequencing data increases 10-fold every 18 months. Whereas first-generation sequencing machines typically generate 0.1 megabases of data per run, second-generation instruments can spew out up to 40,000 megabases in a single run, explains Knudsen. The CLC Genomics Workbench, released in 2008, analyzes data from second-generation HTS instruments. In 2007, the company switched its focus to the analysis of next-generation sequencing data. Right: comparing expression across samples and clustering differentially expressed genes in a heat map Working with RNA-Seq data in CLC Genomics Workbench: Left: mapping of reads showing evidence of expression of three splice variants for this gene. Although designed for first-generation sequence data, he believes that the software makes a good teaching tool for students in molecular biology.

Clc sequence viewer help how to#

When first launched, the software was “a powerful and intuitive way to show people how to do bioinformatics,” says Thomas Knudsen. In the first year, 100,000 downloads occurred, and by 2008, the number of downloads passed one million.

Clc sequence viewer help free#

The present study would provided a foundation for further investigations on the classification and functions of the blueberry BHLH family.The Sequence Viewer software remains free and can be downloaded from the company’s website. PCR results showed that 45 genes were expressed at various developmental stages of buds, stems, leaves, flowers, and fruits, suggesting that the function of BHLH was associated with the development of different tissues and organs of blueberry, Duke. Furthermore, phylogenetic analysis showed that BHLH genes of blueberry (Duke) could be divided into 13 sub-groups. Sequence analysis revealed that 55 genes of that contained a complete BHLH domain. Analysis of the transcriptome library identified a total of 59 BHLH genes. By using COG and GO classification tools, sequences with annotation information were divided into 25 and 52 categories, respectively, which involved transport and metabolism, transcriptional regulation, and signal transduction. Functional annotation showed that 32 244 unigenes were annotated into Clusters of Orthologous Groups (COG) and Gene Ontology (GO) databases, whereas the rest of the 75 789 unigenes had no matching information. The results showed that 28.38 gigabytes of valid data were obtained from transcriptome sequencing and were assembled into 108 033 unigenes. Mega 4, CLC Sequence Viewer 6 software, and quantitative PCR were employed for bioinformatics and expression analyses of the basic helix-loop-helix (BHLH) transcription factors of the sequencing library. The highbush blueberry ( Vaccinium corymbosum) Duke, was used to construct a de novo transcriptome sequence library and to perform data statistical analysis.