MOLECULAR BIOLOGY WORKFLOWS

Software for Molecular Biology and Sequence Analysis

Lasergene Molecular Biology is a comprehensive package of sequence analysis software, for DNA, RNA, and protein sequence data. This package includes all the tools you need to perform multiple and pairwise sequence alignments, identify and annotate genes, assemble Sanger sequences, create virtual clones, design primers, concatenate sequences, find a reverse complement, perform an NCBI BLAST search, and more.

Molecular Cloning  Primer Design  Sequence Editing and Analysis

Sanger/ABI Sequence Assembly  DNA, RNA and Protein Sequence Alignment  Gene Discovery and Annotation

Molecular Cloning

Lasergene Molecular Biology provides comprehensive cloning software. Simulate clones with confidence using our highly accurate and easy-to-use software. For cloning projects, simply select your insert and vector sequences and restriction sites, and SeqBuilder Pro will automatically design PCR primers, recognize recombination sites, identify compatible restriction sites and construct the virtual clone for you.

Automated Virtual Cloning

Make your clone virtually before making it in the lab

  • Supports Gateway, Gateway Multisite, Gibson, GeneArt, In-Fusion, TA, TOPO, or PCR-directed restriction enzyme molecular cloning methods
  • Choose vector sequence(s) from the built-in  catalog or use a custom vector
  • View step-by-step instructions for preparing the vector and amplifying the insert
  • View details about fragment inserts, primers, fragment junctions
  • Save or print instructions for making the clone in your lab
  • Export publication-quality images

Sanger Clone Verification

Prevent costly errors

  • Align Sanger reads to validate insert alignment and orientation of sequenced clones
  • Check and validate your plasmid insertion
  • Catch read misalignment and insertion errors

Automated Plasmid Annotation

Are your plasmid features out-of-date?

  • Auto-annotate your plasmids with accurate, up-to-date features from our curated plasmid vector database.
  • Specify  feature matching stringency parameters
  • Once matches are found, update all  features to the latest version automatically or make choices individually
  • Sortable and interactive annotation results table
  • Add your custom features to the feature library
  • Create colorful, customizable plasmid maps

Primer Design

Lasergene Molecular Biology provides comprehensive primer design software. Create PCR primers and primers for PCR-based cloning methods, as well as sequencing primers that can improve coverage or extend into gaps in a de novo assembly.

Primer Design

Primers that work… the FIRST time!

  • Create primers for PCR-based cloning; to increase coverage or extend into gaps in a de novo assembly
  • Utilize our PCR site-directed mutagenesis workflow, which enables you to see the impact of a sequence mutation on the structure of a protein before designing your primers
  • Select a range of interest guided by feature and ORF information
  • Specify default or custom primer locations, conditions, melting temperature and more
  • View major and alternate primer pairs simultaneously
  • Automatically check for mispriming (dimers and hairpins)
  • Easily modify primers by length, restriction sites, or codon mutations
  • Create and share primer catalogs

PCR Site-Directed Mutagenesis

PCR Site-Directed Mutagenesis in Protean 3D and SeqBuilder Pro

See the structural impact of a mutation before designing your primers

  • Determine desired variants by using Lasergene Protein to scan your protein for “hot-spots” to identify residues that contribute to fold stability, or create amino acid variants and predict protein structural changes
  • Design and mutate PCR primers to introduce desired variants
  • Create expression clones to amplify mutated gene using PCR-based cloning methods

Buy SeqBuilder Pro

All of the sequence editing, annotation, cloning and primer design workflows listed above can be completed in SeqBuilder Pro, a component of Lasergene Molecular Biology which can be purchased online as a single application for as little as $99/year for an academic license.

Buy SeqBuilder Pro Now - Starting at $99!
SeqBuilder Pro Circular Map with Enzymes

Sequence Editing and Analysis

SeqBuilder Pro, part of Lasergene Molecular Biology, allows you to edit DNA, RNA, and amino acid sequences quickly and easily. Take your analysis to the next level with batch editing functions such as reverse translation and  extraction of GenBank style features. The built-in analysis tools allow you to simulate restriction enzyme digests, BLAST gene and protein sequences, and more!

Sequence Editing

Many customizable display options

  • Translate DNA, back-translate protein, reverse complement DNA, and more with manual or automated sequence editing options
  • Apply reading frames and view restriction enzyme binding sites
  • Search for and open sequence matches from NCBI’s BLAST database
  • Use a text query to search for and open sequences from NCBI’s Entrez database
  • Create and edit GenBank style features
  • Create plasmid maps and export publication-quality graphics

Agarose Gel Simulation

Skip the mess with virtual gels!

  • Plot DNA fragment mobility in silico
  • Choose from a huge selection of commercial gels or create a custom gel
  • Add enzymes, primers and/or molecular weight markers
  • Watch “hours” pass in a fraction of a second!
  • Compare your virtual gel with the image simulation to confirm complex banding patterns

Sanger/ABI Sequence Assembly

Lasergene Molecular Biology provides comprehensive support for assembly and analysis of Sanger sequencing data within the SeqMan Pro application. SeqMan Pro allows you to assemble your read data de novo or against one or more reference sequences. You can then use the analysis tools within the application to view read alignment and coverage, assess SNPs and annotate the consensus sequence.

Sanger Sequencing Assembly Features

  • Assemble your reads into groups based on sequence names
  • Trim vector and poor quality data and restore sequence ends
  • Annotate features automatically or manually
  • Design sequencing primers that walk into gaps or improve coverage
  • Export the consensus sequence to other applications for further analysis

 

White papers:

♦ Accuracy of de novo assembly of Sanger trace data: SeqMan Pro vs. three alternative pipelines

♦ Sanger data assembly in SeqMan Pro

DNA, RNA and Protein Sequence Alignment

The MegAlign Pro application in Lasergene Molecular Biology provides DNA, RNA, and protein sequence alignment using a range of pairwise and multiple aligning methods. From the sequence alignments generated, you can quickly create phylogenetic trees as well as reports and tables.

Pairwise Sequence Alignment

Sequence Alignment Features

 

  • Align DNA/RNA (nucleotide) or protein (amino acid) sequences or a combination of these via multiple sequence alignment algorithms including ClustalW, MUSCLE, MAFFT, and Clustal Omega
  • Utilize newly implemented pairwise algorithms: Smith-Waterman (local) and Needleman-Wunsch (global and semi-global) improved with ParaSail hardware optimization
  • Align microbial genomes with Mauve
  • Create sub-alignments from selections
  • Export your sequence alignment to PowerPoint as an editable image for presentations

Multiple Sequence Alignment

Gene Discovery and Feature Annotation

Lasergene Molecular Biology provides automated annotation of plasmids and other sequences, using matches to a curated feature database, as well as gene discovery and annotation tools for novel sequences. Take advantage of our expertly curated database of common plasmid vector features and identify feature matches automatically with SeqBuilder Pro. The software also includes applications for identifying ORFs, spliced junctions, transcription factor binding sites and restriction sites, and for the identification of regions that match user defined DNA or protein sequences.

Automated Sequence Annotation

Automated Sequence Annotation
  • Automatically collect features from sequences and save to your own custom database
  • Annotate new sequences with database features
  • Apply custom feature styles to sets of sequences
  • Annotate large sequences – up to microbial genome size
  • Annotate large batches of sequences

Gene Discovery

  • Predict coding regions using Borodovsky’s Markov method and identifying ORFs. The Borodovsky method finds potential coding regions by analyzing your sequence against statistical matrix files.
  • Predict intron/exon boundaries using species-specific pattern files for splice sites, start sites and transcription factor binding sites.
  • Align known genes, ESTs or proteins with your sequence. The score printed on the region plot indicates how many bases in the two sequences matched.
  • Export your completed, annotated sequences to GenVision to create publication-quality visualizations.

All of the functionality above is included in Lasergene Molecular Biology!

SEE PRICING

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