About PlasmidTools

PlasmidTools is software for managing work with DNA constructs, cloning and open reading frames (ORFs). Easily turn complex sequences into comprehensible maps, create new clone- and subclone maps with a few mouse clicks, design primers for PCR and sequencing, align sequencing data, analyse codon-usage compatibility of ORFs in various species, generate ORFs optimized for expression in selected species, map cut sites and open reading frames, use customizable sequence databases to easily map and annotate features of interest, ++. Everything integrated under the same roof in a multiple-document interface, to make life easy.

PlasmidTools can be installed in Windows 7 and later versions, and is free to install and run.

(Ver. 2.6.0.4)

Program features include:

• Cloning Tool to generate new DNA constructs by a few mouse clicks.
• standard restriction-based cloning.
• Gateway recombination cloning.
• Oligo primer analysis - design primers for PCR and sequencing.
• latest nearest-neighbor thermodynamics.
• primer report with primer-dimer interactions visualized.
• Sequence alignment editor for handling sequencing data.
• aligning algorithm optimized for sequence reads.
• auto-detection of sequence format in opened files.
• Codon-usage compatibility analysis of open reading frames in various species.
• Open reading frame generator for optimal expression in selected species.
• Options to skew codon usage away from G and GC nucleotides and to exclude low-frequency codons.
• Sequence database functionality.
• customizable databases with edit/copy/merge functions.
• pre-made databases (also customizable), incl. antibiotic resistance genes and Gateway sites.
• scan function to find and annotate matching sequences in project files.
• Restriction-site mapping.
• digest report with selected enzymes.
• Open reading frame analysis.
• Translation of open reading frame to protein sequence.
• Hairpin (stem-loop) mapping.
• Sequence search function with adjustable percent-identity threshold.
• Automatic annotating of analysis- and search-results into project file/graphical map.
• Easy switch between upper/lowercase, DNA/RNA, and +/- strands.
• Error check of sequence and annotation syntax.
• Import of plain sequence, FastA, GenBank, EMBL, IG and GCG sequence files.
• auto-detection of sequence format.
• Export to plain sequence, FastA, GenBank and EMBL sequence files.
• Flexible import of other file types by combining copy/paste and automatic cleanup.