Comparison of workbenches
Below we list a number of functionalities that differ between CLC Workbenches and the CLC Sequence Viewer:
- CLC Sequence Viewer ()
- CLC Main Workbench ()
- CLC Genomics Workbench ()
Data handling | Viewer | Main | Genomics | ||||
Add multiple locations to Navigation Area | |||||||
Share data on network drive | |||||||
Search all your data |
Assembly of sequencing data | Viewer | Main | Genomics | ||||
Advanced contig assembly | |||||||
Importing and viewing trace data | |||||||
Trim sequences | |||||||
Assemble without use of reference sequence | |||||||
Map to reference sequence | |||||||
Assemble to existing contig | |||||||
Viewing and edit contigs | |||||||
Tabular view of an assembled contig (easy data overview) | |||||||
Secondary peak calling | |||||||
Multiplexing based on barcode or name |
Next-generation Sequencing Data Analysis | Viewer | Main | Genomics | ||||
Import of 454, Illumina Genome Analyzer, SOLiD and Helicos data | |||||||
Reference assembly of human-size genomes | |||||||
De novo assembly | |||||||
SNP/DIP detection | |||||||
Graphical display of large contigs | |||||||
Support for mixed-data assembly | |||||||
Paired data support | |||||||
RNA-Seq analysis | |||||||
Expression profiling by tags | |||||||
ChIP-Seq analysis |
Expression Analysis | Viewer | Main | Genomics | ||||
Import of Illumina BeadChip, Affymetrix, GEO data | |||||||
Import of Gene Ontology annotation files | |||||||
Import of Custom expression data table and Custom annotation files | |||||||
Multigroup comparisons | |||||||
Advanced plots: scatter plot, volcano plot, box plot and MA plot | |||||||
Hierarchical clustering | |||||||
Statistical analysis on count-based and gaussian data | |||||||
Annotation tests | |||||||
Principal component analysis (PCA) | |||||||
Hierarchical clustering and heat maps | |||||||
Analysis of RNA-Seq/Tag profiling samples |
Molecular cloning | Viewer | Main | Genomics | ||||
Advanced molecular cloning | |||||||
Graphical display of in silico cloning | |||||||
Advanced sequence manipulation |
Database searches | Viewer | Main | Genomics | ||||
GenBank Entrez searches | |||||||
UniProt searches (Swiss-Prot/TrEMBL) | |||||||
Web-based sequence search using BLAST | |||||||
BLAST on local database | |||||||
Creation of local BLAST database | |||||||
PubMed lookup | |||||||
Web-based lookup of sequence data | |||||||
Search for structures (at NCBI) |
General sequence analyses | Viewer | Main | Genomics | ||||
Linear sequence view | |||||||
Circular sequence view | |||||||
Text based sequence view | |||||||
Editing sequences | |||||||
Adding and editing sequence annotations | |||||||
Advanced annotation table | |||||||
Join multiple sequences into one | |||||||
Sequence statistics | |||||||
Shuffle sequence | |||||||
Local complexity region analyses | |||||||
Advanced protein statistics | |||||||
Comprehensive protein characteristics report |
Nucleotide analyses | Viewer | Main | Genomics | ||||
Basic gene finding | |||||||
Reverse complement without loss of annotation | |||||||
Restriction site analysis | |||||||
Advanced interactive restriction site analysis | |||||||
Translation of sequences from DNA to proteins | |||||||
Interactive translations of sequences and alignments | |||||||
G/C content analyses and graphs |
Protein analyses | Viewer | Main | Genomics | ||||
3D molecule view | |||||||
Hydrophobicity analyses | |||||||
Antigenicity analysis | |||||||
Protein charge analysis | |||||||
Reverse translation from protein to DNA | |||||||
Proteolytic cleavage detection | |||||||
Prediction of signal peptides (SignalP) | |||||||
Transmembrane helix prediction (TMHMM) | |||||||
Secondary protein structure prediction | |||||||
PFAM domain search |
Sequence alignment | Viewer | Main | Genomics | ||||
Multiple sequence alignments (Two algorithms) | |||||||
Advanced re-alignment and fix-point alignment options | |||||||
Advanced alignment editing options | |||||||
Join multiple alignments into one | |||||||
Consensus sequence determination and management | |||||||
Conservation score along sequences | |||||||
Sequence logo graphs along alignments | |||||||
Gap fraction graphs | |||||||
Copy annotations between sequences in alignments | |||||||
Pairwise comparison |
RNA secondary structure | Viewer | Main | Genomics | ||||
Advanced prediction of RNA secondary structure | |||||||
Integrated use of base pairing constraints | |||||||
Graphical view and editing of secondary structure | |||||||
Info about energy contributions of structure elements | |||||||
Prediction of multiple sub-optimal structures | |||||||
Evaluate structure hypothesis | |||||||
Structure scanning | |||||||
Partition function |
Dot plots | Viewer | Main | Genomics | ||||
Dot plot based analyses |
Phylogenetic trees | Viewer | Main | Genomics | ||||
Neighbor-joining and UPGMA phylogenies | |||||||
Maximum likelihood phylogeny of nucleotides |
Pattern discovery | Viewer | Main | Genomics | ||||
Search for sequence match | |||||||
Motif search for basic patterns | |||||||
Motif search with regular expressions | |||||||
Motif search with ProSite patterns | |||||||
Pattern discovery |
Primer design | Viewer | Main | Genomics | ||||
Advanced primer design tools | |||||||
Detailed primer and probe parameters | |||||||
Graphical display of primers | |||||||
Generation of primer design output | |||||||
Support for Standard PCR | |||||||
Support for Nested PCR | |||||||
Support for TaqMan PCR | |||||||
Support for Sequencing primers | |||||||
Alignment based primer design | |||||||
Alignment based TaqMan probe design | |||||||
Match primer with sequence | |||||||
Ordering of primers | |||||||
Advanced analysis of primer properties |
Molecular cloning | Viewer | Main | Genomics | ||||
Advanced molecular cloning | |||||||
Graphical display of in silico cloning | |||||||
Advanced sequence manipulation |
Virtual gel view | Viewer | Main | Genomics | ||||
Fully integrated virtual 1D DNA gel simulator |