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NEXT-GENERATION DNA SEQUENCING (NGS)
Sequencher empowers the benchtop scientist by bringing the latest peer-reviewed NGS algorithms out of the command line and into an intuitive point and click interface. Whether performing reference-guided alignments, de novo assembly, variant calling, or SNP analyses, Sequencher has the tools you need to get results. Sequencher has integrated the comprehensive Cufflinks suite for in-depth transcript analysis and differential gene expression of your RNA-Seq data. Sequencher can easily generate unique visualizations of your RNA-Seq data with custom plots and charts giving you publication-ready graphics in seconds.
Your Connections Sessions are automatically saved with your project. With the new Session Launcher, it’s easy to create a new Session, add more data to existing Sessions, or simply review and re-run older Sessions to see if any new sequences of interest have been added to the databases you queried previously. Use the Schematic to provide a graphical overview of your BLAST, Local-BLAST, and Primer-BLAST analyses at the same time. The ability to have multiple Sessions open at the same time means you can view all your results with ease. When your results finally expire from NCBI’s website, you can be sure that they will still be there safe in Connections.
MUSCLE is said to have four major steps in its alignment process. The first step constructs a distance matrix between pairs of sequences using k-mer clustering, this is then converted into a tree. The second step uses this tree to guide a progressive alignment. In the final two steps, the MUSCLE algorithm tries a number of different methods to see if it is possible to improve the tree and hence the multiple alignment.
Compare gene variants to a reference sequence
Confirm vector constructs
Assemble viral and bacterial genomes
Cluster tens of thousands of sequences from cDNA libraries
Assemble cDNA to genomic sequence
Create a primer map
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