on June 21, 2011 by Alastair Kerr in Software Comparisons, Comments (1)

Desktop Sequence Analysis: software review

Shaun Webb, Alastair RW Kerr

A brief summary of the most popular sequence analysis programs in currently in use. All of these programs are compatible with VectorNTI file types so there should be no problem transferring data if you are currently using this software. All are available on at least a free trial. Included is a table of the most common uses for these programs and the functions provided by each package.

Affiliation of Authors: Wellcome trust Centre for Cell Biology, University of Edinburgh



Vector NTI AdvanceTM is a highly integrated, multifunctional desktop sequence analysis application suite. The software contains a comprehensive set of data analysis and management tools, implemented across five application modules that share a graphical user interface. The five modules are:

  • Vector NTI – sequence creation, mapping, analysis, annotation, illustration and management
  • AlignX – multiple sequence alignment of proteins and DNAs
  • ContigExpress – DNA sequence assembly
  • BioAnnotator – functional annotation of proteins and DNAs
  • GenomBench – analysis and annotation of reference genomic DNA sequences

VectorNTI includes a local database, to help you store and manage many types of molecular biology data. Due to the comprehensive range of tools available users may find it difficult to get to grips with at first. It is produced by Invitrogen and primers, vectors etc can be ordered directly through the program. One of its advantages is the link to the S.Pombe database owned by Invitrogen.


GENtle is a software package for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more. It is a free program designed and maintained by Magnus Manske of the University of Cologne. Although functionality is basic compared to commercial packages it still provides most of the tools required for sequence analysis, primer design, virtual gels etc. Graphics are easily manipulated and the interface is easy to use. GENtle is more than adequate for sequence storage, maps and basic analysis and may save you a lot of money. Be aware that the program has not been updated for a couple of years and some bugs do exist.


LaserGene by DNASTAR provides comprehensive software for DNA & protein sequence analysis, contig assembly and sequence project management. The software consists of an integrated suite of seven modules that can be purchased in any combination. The modules of Lasergene are:

  • SeqBuilder – visualization and sequence editing and primer design
  • SeqMan Pro – sequence assembly and SNP discovery
  • MegAlign – sequence alignment
  • PrimerSelect – oligo primer design
  • Protean – protein structure analysis & prediction
  • GeneQuest – gene finding
  • EditSeq – utility for importing unusual file types

The Data Manager enables data integration between the Lasergene modules so that edits, additions and deletions made to a sequence in one module will synchronize and automatically update when opened in most other modules. Lasergene provides all the necessary tools for Sequence analysis, it’s interface is simple and easy to use but not as interactive as some programs. LaserGene is also a favoured package for some of the labs in our institute and is highly recommended by them.


Main Workbench:

Main Workbench comprises all the tools from CLCs DNA, RNA and Protein Workbench programs. The interface is exceptional and intuitive allowing multiple windows and tabs to be open. The program has many useful wizards to guide you through functions such as virtual cloning, it also allows easy import of VectorNTI files. CLC have recently upgraded all of their software for commercial release and Main Workbench performs all the functions you would expect from such a package. It has been noted that some of the additional tools cut back on the options available to the user and are not as powerful as dedicated programs (e.g RNA structure prediction does not allow the user to change temperature, RNA fold is a better tool.). The website tutorials are extremely helpful and work through some of the more common tasks.

Sequence Viewer:

Sequence Viewer is a free stripped down version of Main Workbench utilising the same interface but with a subset of available tools. It is designed specifically for sequence storage, editing and simple analysis. It can be used for restriction site analysis, creating alignments, protein translation, phylogenetics etc. If you simply want a program for storing and viewing sequences then this is ideal.


MacVector is a comprehensive application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a wide variety of other functions. MacVector is often sited as the most intuitive, easy to use program available for sequence analysis and is championed by Mac users. It is not cross platform and this is its biggest drawback.

Geneious Pro

Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis, contig assembly, primer design and cloning, access to NCBI and UniProt, BLAST, protein structure viewing, automated PubMed searching, and more.

Comparison Grid

GENtle VectorNTI LaserGene CLC Sequence Viewer CLC Main Workbench MacVector Geneious
Database SQLITE or MySQL VectorNTI local db, or create your own. No DB, save as files or projects. Hierarchical file/folder structure. Multiple Workspaces. Database sold seperately. Hierarchical file/folder structure. Multiple Workspaces. Database sold seperately. Save as files. Database in development Save as files. Can create a DB and connect to it.
Platform Windows, Mac, Linux (32-bit) Windows (or Mac running windows.) Windows, Mac Windows, Mac, Linux Windows, Mac, Linux Mac only Windows, Mac, Linux
Support Online manual Online manual and video tutorials + support team Online manual and video demos + support team Online manual and video tutorials(good) + support Online manual and video tutorials(good) + support team Online manual + support team Online manual and video demos + support team
Updates Infrequent Regular Regular Regular Regular Regular Regular
GENtle VectorNTI LaserGene CLC Sequence Viewer CLC Main Workbench MacVector Geneious
Map * * * * * * *
Edit Sequence * * * * * * *
Restriction Site Analysis * * * * * * *
Features * * * * * * *
Orfs * * * * * * *
Translation * * * * * * *
GENtle VectorNTI LaserGene CLC Sequence Viewer CLC Main Workbench MacVector Geneious
External Databases
BLAST * * * * * *
Database Sequence Retrieval Entrez Entrez Entrez + UniProt Entrez + UniProt Entrez Entrez
RNA fold prediction *
Virtual Cloning Manual(limited/tedious) * * * * *
GENtle VectorNTI LaserGene CLC Sequence Viewer CLC Main Workbench MacVector Geneious
Plots * * * * * *
Proteolysis * * * * *
3D Viewer * * *
Virtual PCR * * * * * *
Primer Design * * * * * *
GENtle VectorNTI LaserGene CLC Sequence Viewer CLC Main Workbench MacVector Geneious
View Files * * * * * *
Assembly * * * Can align contigs to a ref. sequence *
Additional Next Gen. Software available Seq Man NGen Genomics Workbench Genomics Workbench Assembler
GENtle VectorNTI LaserGene CLC Sequence Viewer CLC Main Workbench MacVector Geneious
Alignment * * * * * * *
Algorithm Clustal-W,Smith-Waterman,Needleman-Wunsch Modified Clustal-W Many including Clustal-V/W Progresive alignment based on Feng & Doolittle. 2 options (fast and accurate) Progresive alignment based on Feng & Doolittle. 2 options (fast and accurate) Clustal-W Muscle, Clustal W, custom
Virtual Gel * * * *

1 Comment

  1. Jack

    April 5, 2012 @ 10:35 pm

    Anybody reviewing Staden Package v2 and Ape v2?

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