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Lasergene® V8.0

A from Comprehensive Software for DNA & Protein Sequence Analysis, Contig Assembly and Sequence Project Management - Now with expanded Next-Generation Sequence Assembly and Analysis Capability

Compatible with Windows® Vista® and XP as well as Mac OS X 10.5 and 10.4.

Lasergene v8.0 has added Features that simplify Primer Design, SNP analysis and protein structural analysis. New primer designing capabilities that have been added to SeqBuilder simplify mutagenesis and virtual cloning.

Lasergene software consists of core functionality built on the DataManager and Seqbuider. 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.

Users can assemble from a few sequences to bacterial-size genomes into contigs. SeqMan Pro further expands user capability by being able to import .sff, .fna, .fas and .qual files from Roche 454 Life Sciences™ and to generate advanced Flowgram histograms. Users can also work with Illumina®, Roche 454™ and/or Sanger data.

DNASTAR Lasergene 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
GeneQuest    : Gene finding
Megalign       : Sequence alignment
PrimerSelect : oligo primer design
Protean        : Protein structure analysis & prediction
SeqManPro : sequence assembly and SNP discovery
EditSeq        : Utility for importing unusual file types.

SeqBuilder

Visualization and sequence editing

Automated Virtual Cloning

Create a New Cloning Project

Select the method you wish follow and the software will provide the appropriate vector selection from the laserGene Vector Catalog

The wizard will construct the Virtual clone automatically once the ends and the vector selected are correct

» Flexible User Interface and Graphic Display

» Integration with other Lasergene applications

» Editing and Analysis

Translate DNA or back translate protein using any of the supplied genetic codes or customize your own.

Choose restriction sites to display based on any combination of: Manual selection of enzymes, Frequency of cuts, Type or class of enzyme, Site complexity, Overhang compatibility.

View ORFs that are updated with every sequence edit

» Sequence Entry

Import data from many popular file formats

Download sequences directly from NCBI* or a DNASTAR StarBlast database using accession numbers, BLAST, or text searches

GeneQuest

Gene Discovery and Sequence Annotation

GeneQuest is a fully integrated module of Lasergene that assists users to locate genes, regulatory elements, patterns and structure in your primary DNA sequence. GeneQuest’s comprehensive set of analytical methods can be easily applied and manipulated for projects of any size – small, BAC-sized or even larger. Users can easily compare sequences with existing genome and Expressed Sequence Tags (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 won use or for publication or submission to public databases.

New Features added with Lasergene v8.0 increase the visualization, analysis and customization of screens for specific projects. Improvements include:

Identifying and Annotating Coding Regions

Improve export to Genvision for higher quality graphic images.

Display a larger number of Features.

Increased sorting capability to better customize your analysis.

Ability to customize screen to match your project needs.

GeneQuest Features

» Sequence Entry

Import data from many popular file formats

Read sequences and features from other Lasergene project files

Edit template sequence and share newly created feature through integration with Seqbuilder and other Lasergene modules

Download sequences directly from NCBI or other BLAST servers using accession numbers, BLAST or text searches.

» Gene Finding

Predict coding regions using Borodovsky’s Markov method

Predict intron/exon boundaries using species-specific pattern files for splice sites

Align known genes, ESTs or proteins with your sequence

Predict where genes start using species-specific pattern files for start sites and transcription factor binding sites

Locate ORFs, stops and starts

Submit any selected feature, segment or all of your sequence as a BLAST query

Investigate related sequences using keywords with the integrated Entrez search tool

» Structure and Composition

Display restriction sites

Locate direct, dyad and inverted repeats

Generate codon usage summaries

View simulations of agarose gel separations of restriction digests

Generate and graph base distribution summaries

Plot base frequency and base skew

Predict RNA folding

Plot localized DNA bending

» Graphical Displays

Juxtapose or superimpose related analysis methods or displays

View project at base level and at full overview magnification simultaneously

Display data as graphs or boxes indicating a range

Customize line colors, fill patterns and fill colors for all display objects

Display features in a variety of shapes

Name individual segments for identification ease

MegAlign

Multiple and Pairwise Sequence Alignment

MegAlign offers researchers a choice of four pairwise and four multiple sequence alignment methods for aligning nucleic acid or polypeptide sequences. Users can enter their own sequences or load public data directly from NCBI. To find more related sequences for alignment, a BLAST query can be run or the Entrez text query interface can be utilized, followed by dropping in the sequences wanted from the list of matches.

Alignments views can be customized to highlight the similarities or differences of the sequences. Differences in chemical, structural, or functional characteristics between sequences, researchers’ groupings or consensi can be displayed. Researchers can construct phylogenetic trees, generate detailed numerical reports, or export data of sequence comparisons. MegAlign provides valuable tools permitting comparisons of gene families or sequence pairs that can be customized for presentations and publications.

MegAlign Features

» Sequence Entry

Import data from many popular file formats

Read sequences and features from other Lasergene project files

Edit template sequence and share newly created features through integration with Seqbuilder and other Lasergene modules

Download sequences from NCBI using accession number, BLAST or text search

» Alignments and Analyses

Align DNA, protein and DNA+protein sequences

Perform multiple sequence alignments using :

» Multiple Sequence alignments



» Pairwise Alignment

Create sub-alignments from selected ranges of longer alignments

Reconstruct phylogeny

Calculate sequence similarity and distance

Edit an adjust final alignment manually if desired

Export data and alignment into popular formats

» Graphical Displays and Tools

Customize alignment displays

Highlight matches or mismatches to the consensus or other sequence with distinct colors or shading

Define the consensus by residue or by chemical, structural or charge characteristics

Create a custom consensus based on researcher’s own residue classification scheme

Display consensus strength as color-coded histograms

Copy selected sections of alignment report and paste into other applications

Notes on Bootstrapping

PrimerSelect

Oligonucleotide Design and Analysis

» Customize Primer Design and Editing

Adjust parameters such as primer and product length, primer locations, Tm, hairpins or use the default settings

Determine the best primer pairs or best probes for varied conditions

Analyze existing primers

Create degenerate, inosine-containing and "bestguess" primers from ambiguous templates

View the effects on restriction sites and translations when editing primer sequences

Select from a list of alternative codons for silent mutations or specific residue changes
Graphical and Tabular Displays

Choose an overview of primers located on your template or view the sequence at base level with graphs of Tm and G on both strands

Analyze tables of amplification details, primer base compositions, primer lengths, Tm and G

Protean

Protein Structure Prediction and Annotation

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, elegant 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 easily annotate and export your findings as reports, pictures or tables.


New Featuresadded with Lasergene v8.0 include interface updates to handle and display larger numbers of Features. Lasergene v8.0 has also added support for an updated Prosite database to find matches to your sequence.

Protean Features
» Protean Images and Displays

Display a larger number of Features.

Simplified export to Genvision.

Increased sorting capability to better customize your analysis.

Updated Prosite database.

Implement protein profile pattern searches.

Ability to customize screen to match your project needs.

» Sequence Entry

Import data from many popular file formats

Read sequences and features from other Lasergene project files

Download sequences directly from NCBI* using accession numbers, BLAST or text searches

Edit template sequence and share newly created features through integration with SeqBuilder and other Lasergene modules

» Structure Analysis Methods

Choose from any of four methods for recognizing alpha helix, beta sheet, turns and coil structures

Predict antigenicity using any of four unique methods

Estimate surface probability using the Emini method

Predict flexibility using the Karplus-Schultz method

Evaluate hydropathy using any of three different methods

Predict amphiphilicity using Eisenberg's method

Estimate charge density

» Locating patterns and related sequences

Locate known sites using Prosite pattern searching

Predict Proteolytic digestion sites

Display numerical data as graphs or boxes indicating values above a threshold Produce secondary structure models

Choose line colors, fill patterns, and fill colors for all display objects

Display features in a variety of shapes and name individual segments

Produce tabular summaries

Utilize specialized chemical and space-filling fonts

Produce secondary structure models

SeqMan Pro

Sequencing Manager, Sequence Assembly, Contig Management, and SNP Discovery

» Refine Data and Customize Assembly Parameters

Remove contaminant sequences such as vector and E. coli automatically

Trim poor-quality trace data automatically using trace quality evaluation

Customize assembly parameters for your own data sets

Set a minimum length parameter to exclude shorter sequences

» Display and Refine the Assembly

Use the trace quality evaluation method to achieve the most accurate consensus possible

View multiple consensus sequences, sequences, traces and six-frame translations aligned in a single window

Compare consensus sequences generated by trace evidence, majority and Phrap methods

Detect SNPs and conflicts

Force particular bases or sequences to be used for the consensus

Display 454 assemblies in flowgram

Reintroduce trimmed data easily and immediately view the effects on the consensus

Reassemble contigs using alternative assembly parameters

Assemble sanger and next generation sequence data

» Primer Walking - Design primers to improve the coverage

The new Primer Walking feature in SeqMan identifies weak coverage and sequencing gaps and helps you design sequencing primers to cover these regions

Design sequencing primers that extend upstream and downstream from an existing contig and walk into a region with weak or poor representative trace data

» SNP Discovery

Add sample sequences to a project and select a reference sequence against which to compare all others for variation

Discover homozygous and heterozygous SNPs

Confirm or reject that bases are actual SNPs

Generate SNP reports that enable further genetic analysis of the sequence sample population

» Use SeqMan Pro when

Your data set is large. The time to assemble is far less.

You have repeated sequences in your dataset. Using the Use Repeat Handling function and the Match Percentage calculation helps prevent repeated regions from assembling together incorrectly.

You have data with noisy ends. Use the Maximum Mismatch End Bases parameter to ignore the noisy ends.

You are doing SNP analysis. Gapped regions are aligned more accurately.

EditSeq

Utility for Editing and Importing Unusual File Type

» Sequence Entry

I.U.B. nucleotide and protein codes fully supported Import data from many other programs

Proofreading by voice read back

Keyboard entry and configuration for alphabetical or numeric control

Feature coordinates automatically updated with sequence editing

» Analysis

Reverse complement sequence

Translate DNA

Backtranslate proteins

Statistics for DNA and proteins

Control and customize expression-specific codes

Integrated BLAST and Entrez text searches* search tools

Copy/paste sequence includes contained annotations

» Display

Sequence, comments and annotations in separate, editable panes

Feature creation utilizing NCBI's applicable feature keys

Exon selection by triplet indicator

ORF identification and selection

Sequence and annotations dynamically linked

NEW RELEASE - Lasergene® V8.0

The latest version of Lasergene offers users a number of improvements and enhancements over previous versions. New features included in Lasergene 8.0:

Full Annotation Support with Enhanced SNP Reporting and Analysis
Enhancements to the SeqMan Pro module now permit users to study SNP codons, to easily filter SNPs reported depending on your experimental needs, to permit creation of new features and to perform larger assemblies faster.

Simplified Primer Design to Shorten Time spent on Virtual Clone Design
Primer Design capabilities have been added which allow design and modification of a primer and the cutting and cloning of the PCR insert into a vector.

Direct export to Genvision
This expands and simplifies genomic mapping and comparison studies and provides support for outstanding publication-quality visualizations.

Read Roche 454 Life Sciences™ output files (*.sff, *.fna, .fas and *.qual types)
Pyrosequencing techniques offered by 454 Life Sciences offer the most established applications in this area. Researchers can import file formats directly from 454, use along with Sanger sequencing methods and take advantage of the analysis tools of Lasergene.

Maximum Expected Coverage (MEC)repeat region analysis
New parameter permits the user to designate a maximum depth of coverage value. In the Strategy View, areas exceeding the Value are illustrated as thick red line segments.

View Flowgram diagrams for Roche 454® assembly visualizations
Flowgram diagrams using *.sff output can be generated (below). Base calls and Quality scores for each call are optionally shown within the histogram. Bases called are listed in the second row.

Fully compatible with Windows Vista™
Lasergene v8.0 is fully tested and compatible with Windows® Vista™, XP and 2000, in addition to Macintosh® OS 10.5 and OS 10.4.

GenVision

GenVision creates images of large quantities of data, so you can conveniently display annotations or comparisons of different data types. GenVision, which has already been used to publish a number of annotated genomes, has proven to be a very flexible and powerful tool for visualizing large or complex data sets. In addition to annotated genomes, GenVision can also be used visualize data comparisons.

The GenVision Plug-in for Adobe® Illustrator® - A completely graphical approach

GenVision “Plug-in” allow you to create genomic images within the Adobe Illustrator program and to view the image in real time as you add data and make changes. The GenVision plug-in is suitable for those who wish to use Illustrator graphical interface forcreating images.

The GenVision Standalone application
The GenVision standalone application is an independent, window-based program that has the image creation capabilities of the GenVision plug-in but doesn’t display the image. The image is built by collecting and arranging data files, then creating a post script file. You then use another application to view the post script image-DNAATAR recommend GSView, which is a freeware. The standalone version of genvision is suitable for users who have very large data sets.

ArrayStar® V3.0

Microarray Gene Expression Analysis

ArrayStar v2.1 provides a wide range of analytical and visualization tools that will assist researchers in interpreting results obtained from gene expression runs. Data files from Affymetrix, Illumina and Roche NimbleGen can be directly read. Importation of .txt files give users the capability of analyzing spotted array runs and data from other sources.

Several NEW Features have been added to v.2.1 that simplify the process of gene expression data analysis. Foremost of the Features is the expansion of the types of data that can be used with the system. As in the earlier version, Normalized data can be used. Version 2.1 has added a Normalization feature that permits users to easily use either RMA, PLIER ( for use with Affymetrix data) or Averaging Summarization (simple normalization).


» Arraystar Features

Compatible with Affymetrix and NimbleGen normalized data files

Import wizard supports .txt files

Conducts a wide range of analyses and visualizations to evaluate expression patterns

Identifies genes with similar expression patterns

Clusters images to identify groups of co-regulated genes

Reveals gene expression level plots with Line Graphs and Thumbnails

Displays expression levels of many genes across multiple experiments with a heat map

» ArrayStar Applications

Expression Profiling

Identify expression patterns of genes

Identify relative expression levels of genes

Identify groups of co-regulated genes

Visualize clusters of co-regulated genes

Identify differentially expressed genes

Annotate for grouping of genes by functionality

SeqMan NGen (SNG) - V1.2

Software for Next Generation sequence assembly of Illumina, Roche 454 Life Sciences and Sanger data integrating with Lasergene Sequence Analysis software for analysis and visualization capabilities.

SeqMan NGen uses a unique algorithm to assemble fragment data sequenced using Illumina, Roche 454 and Sanger technologies on a desktop computer. The software can be used in a wide range of genomic assembly and re-sequencing types of Next Generation Sequencing projects.

Because the industry is changing very rapidly, additional capabilities have been added to this version that were not available for the introduction of SeqMan NGen in January 2008. The strength of SNG continues to come from its ability to permit a user to assemble multiple sequencing platforms and to be able to work with a commonly known sequence analysis software suite, Lasergene, for the pre- and post- assembly analysis.

Key Features of SNG include:

Desktop computer (Win or Mac) assembly for Illumina, Roche 454 and Sanger platforms

The software can be used in a wide range of genomic assembly and re-sequencing types of Next Generation Sequencing projects.
o Templated assemblies
o Deep “resequencing” projects where coverage can range from 2 X to over 200,000 X
o De novo genomic assemblies
o RNA-Seq, SAGE and Digital Gene Expression Data Assemblies to multiple short probe reference sequences
o Rapid and accurate trimming and assembling EST data

RAM-dependent assembly method permits efficient assembly of genomes from prokaryotic organisms

It helps in discovering SNPs, Management and Analysis

Full technical support by DNASTAR.

User can annotate their template sequence in SeqBuilder, GeneQuest or SeqMan Pro for known SNPs/variations and other features and generate reports highlighting the SNPs of interest

SNG offers complete flexibility in adjusting assembling parameters to meet the needs of your specific data set

“Users may select a number of preprocessing options, including vector and end-trimming along with the ability to exclude known repeats and contaminant sequences, such as primer reads,f-rom your assembly”.

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