Navigate to where your sequences are stored on your computer.You can import many file types but in this tutorial we will look at importing trace files for further analysis.įile | import or click the import icon on the tool bar. Importing data: Allows you to bring sequenced data into CLC from where it is stored on your computer.Name the folder “My_folder” or a name of your choice and press enter. click on the new folder icon on the tool bar.Creating a folder, it is best to organize data in the navigation area in folders.View area is the main window to the right, where data is viewed and manipulated.Navigation area is where all the data imported into CLC is kept.The user interface of CLC is as below: there is Navigation area and a View area. Download the workbench from the link provided above.It consists of a multiple sequence alignment of sequence reads plus a consensus sequence.Ĭonsensus sequence: A sequence of nucleotides in common between regions of homology in related DNA sequences. This can be more difficult if the region of overlap is very small.Ĭonflict: a nucleotide position in the assembled sequence overlap which has different bases, or where there is a gap on one sequence and a base at the corresponding position on the other sequence.ĭNA Contig: Contiguous sequence of DNA created by assembling overlapping DNA sequence reads. Parts of this article were reprinted from CLC bio.Sequence assembly: aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence.Īssembly to a reference sequence: assembly of the sequenced fragments using a similar sequence (a reference sequence) as a guide.ĭe novo assembly: assembly using only your sequenced fragments. To access CLC Main Workbench or CLC Genomics Workbench, visit Licensed Tools on the HSLS Molecular Biology portal.įor more information about CLC bio resources, call Ansuman Chattopadhyay at 41, Carrie Iwema at 41, or contact Ask A MolBio Librarian. Epigenomics: ChIP-seq analysis, peak finding and refinement, false discovery rate and background distribution tables and graphs.Transcriptomics: digital gene expression based on RNA-Seq, including a wide range of downstream gene expression analyses, novel transcript/exon discovery, interactive view of assemblies and derived gene expression data.Genomics: whole genome re-sequencing and targeted re-sequencing of genomes of any size and type, de novo assembly of an unlimited number of reads, SNP and DIP detection, identification of genomic rearrangements.Other bioinformatics features: multiple alignment of DNA, RNA, and proteins, sequence editor, local complexity region analysesĬLC Genomics Workbench is a cross-platform desktop application that incorporates cutting-edge technology and algorithms for analyzing and visualizing next generation sequencing data.Project and data management: detailed history log, full integration of data input, data management, calculation results, and data export Database searches: GenBank Entrez, BLAST on local databases, PubMed.Pattern search: motif searches for basic patterns, using regular expressions, and/or with ProSite patterns.Protein sequence analysis: antigenicity, PFAM domain search, transmembrane helix prediction, proteolytic cleavage detection RNA structure analysis: secondary structure prediction, symbolic representations.DNA sequence analysis: primer design, in silico PCR, cloning, SNP annotation, restriction enzyme analysis and management.Expression analysis including digital gene expression: support for both microarray and sequencing-based expression data, clustering algorithms, tools for Gene Set Enrichment Analysis. ![]() Noteworthy features include but are not limited to: CLC Main Workbench supports researcher’s daily bioinformatics needs and CLC Genomics Workbench handles sequencing data from high-throughput sequencing systems.ĬLC Main Workbench is an integrated software package that enables users to perform advanced DNA, RNA, and protein sequence analyses, combined with gene expression analysis, seamless data management, and user-friendly graphical viewing and output options. The HSLS Molecular Biology Information Service recently licensed two new bioinformatics resources from CLC bio.
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