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 | ![]() |
![]() |