CLC Main Workbench v.5.6.1

CLC Main Workbench 5.6.1 provides you with a software environment which enables users to make a large number of advanced DNA, RNA, and protein sequence analysis, combined with gene expression analysis, smooth data management, and excellent graphical viewing and output options.CLC Main Workbench includes user friendly gene expression analysis with all features of CLC Protein Workbench, CLC RNA Workbench, and CLC DNA Workbench in one integrated software package.Major Features:Expression analysis including digital gene expressionSupport for both microarray- and sequencing-based (RNA-Seq) expression dataVisualization: Interactive heat map, table and scatter plot viewsTransformation and normalization toolsQuality control tools including principal component analysis, MA- and boxplotsExperimental design tools for two- or multiple group comparisonsT-tests and ANOVA analysis with support for paired/repeated measuresMultiple testing corrected p-values (Bonferroni and/or FDR)Clustering algorithms: hierarchical clustering, k-means and Partitioning Around Medoids (PAM) with support for various distance and linkage measures.Ability to import NetAffx annotation arrays and adding annotation to experimentsTools for Gene Set Enrichment Analysis (GSEA) and for Hyper-Geometric based tests for overrepresented annotation categories (e.g. 'GO'stats or specific protein pathways).Ability to work with Expression Arrays and RNA-seq results at the same time, enabling comparison of resultsDNA sequence analysisEditor for graphically and algorithmically advanced primer designIn silico PCRAssembly of DNA sequence dataMultiplexing - Process Tagged Sequences has an option to filter away groups with few sequences.Molecular cloningGateway CloningAutomatic SNP annotation of sequencesLocal complexity region analysesReverse translation from protein to gene, based on translation tables from a number of speciesAdvanced restriction enzyme analysis and managementDot plot based analysesDNA statistics report including a number of characteristics of a given moleculeNCBI sequence data searchAccess to web info from PubMedRNA structure analysisSecondary structure predictionGraphical view and editing of secondary structureTabular view of structures and energy contributionsSymbolic representation in sequence viewProtein sequence analysisIntegrated 3D molecule viewTransmembrane helix predictionAntigenicitySecondary protein structure predictionPFAM domain searchWeb-based prediction of signal peptides and their cleavage sites (SignalP located on http://www.cbs.dtu.dk/services/SignalP/)Hydrophobicity analyses and graphsProtein charge analysis and graphsReverse translation from protein to gene (a number of translation tables)Interactive translations of DNA and RNA to protein (both single sequences and alignments)Proteolytic cleavage detectionReport of protein statistics (one or more proteins in each report)Comprehensive report including a range of protein analyses in one documentPattern searchSearch for sequence matchesMotif search for basic patternsMotif search using regular expressionsMotif search with ProSite patternsPattern discovery (unknown patterns)Database searchesWeb-based sequence search using BLASTBLAST on local databasesBuild local BLAST databasesGenBank Entrez searchesUniProt searches (SwissProt/TrEMBL)PubMed lookupWeb-based lookup in UniProt, NCBI, and GoogleSNP annotation using BLASTProject and data managementFull integration of data input, data management, calculation results, and data exportDetailed history logAll types of files can be saved in local projects, and launched from the programImport and export of data in a large number of file formatsOption of working in several active workspaces at a time, enabling simultaneous work on multiple projectsOther bioinformatics featuresDNA, RNA and protein sequence editor displaying both linear and circular moleculesMultiple alignment of DNA, RNA, and proteins

CLC Main Workbench 5.6.1 provides you with a ...

clc, solutions, hardware, software, workbench, dna, protein, bio, fpga