DNASTAR Lasergene 7.2

Category Cross-Omics>Sequence Analysis/Tools

Abstract Lasergene is comprehensive software for DNA & Protein sequence analysis, contig assembly and sequence project management. Lasergene is an integrated suite of seven (7) modules that can be purchased in any combination.

The modules are:

1) SeqBuilder - sequence editing, visualization and automated virtual cloning;

2) SeqMan Pro - sequence assembly, primer walking and SNP discovery;

3) MegAlign - multiple sequence alignment;

4) PrimerSelect - oligo design;

5) Protean - protein structure prediction;

6) GeneQuest - gene discovery;

7) EditSeq - utility for importing unusual file types.

Note: 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.

1) SeqBuilder - enables you to edit nucleic acid and amino acid sequences and view the sequences and related items in multiple ways. SeqBuilder's window can be split into multiple panes so that more than one view can be displayed at any time. The possible views include a residue-specific view, a linear map, a circular map, a compact map of restriction cut sites (mini map), as well as a list of features, a summary of all restriction cut sites, and any comments. Each view lists a number of items that can be individually turned on or off including features, restriction sites, translations in all six reading frames, open reading frames (ORFs), and rulers. Many of these items can also be positioned and modified to emphasize certain characteristics. Dynamic links between the sequence and its annotations automatically update feature coordinates when you edit a sequence. Available functionality also includes the ability to reverse complement, translate, back-translate sequences, identify ORFs and perform Basic Local Alignment Search Tool (BLAST) and Entrez (a Global Query Cross-Database Search System) text searches directly to National Center for Biotechnology Information (NCBI) or your personal DNASTAR StarBlast Server (sold separately).

SeqBuilder's editing capabilities are also integrated into many other Lasergene modules. Edits made in SeqBuilder will be shared automatically with other Lasergene applications that are analyzing the same data, making SeqBuilder an integral member of the powerful Lasergene suite.

2) SeqMan Pro - enables you to assemble fragment data from sequencing projects of any size - from a few fragments to hundreds of thousands of fragments - at the push of a button. It also removes unreliable data, including poor quality ends, sub-minimal length reads, and vector and contamination host sequences in a single pass, then assembles the trimmed data and calls the consensus.

SeqMan provides two different assembly methods: the Classic assembler, and the Pro assembler. The Classic assembler should be used when:

In general, the Pro assembler should be used when your data is:

The addition of the new SeqMan Pro assembly algorithm provides Lasergene with the tool necessary to assemble bacterial size genomes using 454 Life Sciences' pyrosequencing technology.

SeqMan uses DNASTAR's unique trace quality evaluation method to call the most accurate consensus sequence possible. A Maximum Expected Coverage (MEC) feature allows users to select the depth of coverage for an assembly and to visually identify areas where the coverage exceeds the selected level. SeqMan also uses dual-end sequence data when available to group and order contigs, allowing you to fill gaps quickly with minimal additional sequencing efforts.

3) MegAlign - offers you a choice of four (4) pairwise and four (4) multiple sequence alignment methods for aligning nucleic acid or polypeptide sequences. Enter your own sequences or load public data directly from NCBI. If you want to find more related sequences for alignment, simply run a BLAST query or utilize the Entrez text query interface, then drop in the sequences you want from the list of matches. Easily customize views of alignments to highlight the similarities or differences of the sequences. Differences in chemical, structural or functional characteristics between sequences can also be displayed as well as your own groupings or consensus. You may create a subalignment from the current alignment by simply selecting a sub-region. MegAlign also enables you to construct phylogenetic trees, generate detailed numerical reports or export data of sequence comparisons. Whether you want to compare gene families or sequence pairs, MegAlign provides you with flexible tools for customizing output for presentation and publication.

4) PrimerSelect - its comprehensive set of tools enables you to design and analyze primers for Polymerase Chain Reaction (PCR), sequencing, probe hybridization and transcription. Enter your own primers or let PrimerSelect generate a sorted list of suggested primers for all or part of your DNA, RNA or back-translated protein template. You can accept PrimerSelect's top choice, evaluated on the thermodynamic properties for annealing reactions, or view all of the options and choose alternatives based on your specialized knowledge. PrimerSelect includes the WorkBench where you preview the effects your choices will have on reading frames and restriction sites. PrimerSelect further assists you by highlighting potential pitfalls in both standard and multiplex PCR experiments via illustrations, graphs and statistical reports. PrimerSelect also lets you perform BLAST or Entrez text searches and load sequences directly from NCBI's databases.

5) Protean - helps you predict and display patterns, secondary structural characteristics and physicochemical properties of protein sequences via its comprehensive suite of protein analysis tools. Protean's simple, advanced graphical user interface can also help you locate antigenic determinants and predict protease digestion patterns. When you find interesting structures, you can utilize the integrated BLAST Tool to search NCBI's databases for related sequences using all or part of your polypeptide as the query. Protean also provides you with the tools to annotate and export your findings as reports, pictures or tables.

6) GeneQuest - helps you locate genes, regulatory elements, patterns and structure in your primary DNA sequence. GeneQuest's comprehensive set of analytical methods can be applied and manipulated for projects of any size - small, BAC-sized (a long genomic query sequence) or even larger. You can easily compare sequences with existing genome and Expressed Sequence Tag (EST) data using the integrated BLAST feature, and find out more about related sequences using the integrated Entrez search tool. GeneQuest also provides annotation and visualization tools so you can document your discoveries for your own use or for publication or submission to public databases.

7) EditSeq - is provided with every Lasergene system to enable you to work on nucleic acid and protein sequences of all sizes from a variety of formats including GenBank, FASTA, MacVector, Genetics Computer Group (GCG), Text, Applied Biosystems (ABI), and data from the clipboard. You can also access NCBI's databases by accession number or utilizing the integrated internet interface to search BLAST and Entrez text databases. With EditSeq you can manually edit sequence, comments and annotations, conveniently separated into three panes. Dynamic links between sequence and annotations exhibit automatic updating of feature coordinates with sequence editing and inclusion of features with copying/pasting of sequences. Available functions include reverse complement, invert, translate, back- translate, and ORF identification.

System Requirements

Lasergene 7.2 for Macintosh

Lasergene 7.2 for Windows®

* RAM requirements vary depending on size of data being analyzed. At least 512MB RAM is recommended for SeqMan Pro Assembler.

Manufacturer

Manufacturer Web Site DNASTAR Lasergene

Price Contact manufacturer.

G6G Abstract Number 20071

G6G Manufacturer Number 100770