Clone Manager 12

Professional EditionCloning, graphic maps, primer design, sequence alignment -- Version 12 for Windows
Clone Manager Professional provides a comprehensive,
fully integrated set of tools for enzyme operations, cloning
simulation, graphic map drawing, primer design andanalysis, global and local sequence alignments, similarity
searches, and laboratory-sized sequence assembly projects.
You can also use Clone Manager as a quick and easy way
to view or edit sequence files, find open reading frames,
translate genes, find genes or text in files, or organize
primer collections.
Use the Clone Share system to share molecules.

Simulate Cloning••••Cut, ligate DNA, modify molecule ends
New multiple-molecule Ligate window
Cloning Wizards for current PCR-based techniques
Plan Cloning Wizard for restriction enzyme cloning

Draw Graphic Maps•••

Clone Manager can cut DNA at enzyme cut sites or atuser-specified basepair positions. Molecule features andenzyme sites are automatically recalculated after a cutoperation. The program can ligate DNA, checking forcompatible ends. You can modify molecule ends, ifneeded for ligation, and select the cloning orientation.
For fast simulated cloning, you can cut, ligate, and modify
ends -- all from the same Ligate display window showing
sticky ends and molecule icon maps.

Prepare high-resolution graphic maps
Print, copy to clipboard, export to file
Enhanced Views of graphic map

Prepare high-resolution circular or linear graphic maps.
Control styles and colors for feature types and enzyme
sites; control map size and position. For your lab
notebook, select to print the map with associated text
(description and notes; map features and enzyme sites) .
For a publication or presentation, use an Enhanced Viewof the graphic map to customize a special molecule map.
Set individual feature styles, colors, patterns, positions.
Drag feature names to reposition, if needed. Removeenzyme sites or features from a map without modifying
the original molecule data. Save enhanced views in themolecule file (maximum 6 views/file). Print, copy, export
in vector or raster (Tif, Png, Gif, bitmap) formats.

Work with Enzymes•••

Find enzyme sites, view enzyme information
Do restriction enzyme analysis
Create user enzyme lists, transient lists

Clone Manager scans the sequence and identifies enzyme
recognition sites, drawing an accurate on-screen working
map. Click tabs at the bottom of the molecule viewer
window to see the map, restriction map data, sequence,features, or molecule information. Zoom to transiently
view just a portion of a larger molecule.

Use cloning wizards to help you to simulate cloning using avariety of current cloning techniques: Gateway Recombination Cloning, Topo Cloning, Gibson Assembly, InFusion Cloning, Ligation-Independent Cloning or related
cloning techniques.
The wizards will help you select the appropriate components, show you the proposed result, and create the final
recombinants. You can assemble a set of overlapping
fragments, previously prepared, or use PCR to create
amplified fragments with overlaps, then assemble thefragments. Save recombinant molecules, primers.

Scrolling map sites list shows enzyme sites, primer sites,label sites or features. A fast and powerful restriction
enzyme analysis module has five display styles, including
a list of No-Cutters. Filter to see only the results youneed. View enzyme properties, suppliers, isoschizomers,or compatible ends information. Update enzyme lists
monthly using REBASE files.

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Email sales@scied.com·Phone (919) 386-1027

Design Primers

Primer Operations

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Search for primers and list results
Position primer in molecule sequence and evaluate
Use the Sequencing Primer Wizard

Search for PCR primers or pairs, sequencing primers, orprobes. Sort results lists by rank (quality) or position, orview summary of search progress showing which criteria
eliminated primers.

Find primers that bind to your molecule
Find molecules with sites for your primer
Primer Values, Mutagenesis Profiles

Scan the primers you have created to find which could
bind effectively to a molecule of interest. Primer sites canbe added to molecule files and displayed on the molecule
map or formatted sequence. Or scan molecule files on
your computer or local network to look for molecules thathave binding sites for a primer of interest.
Use the Primer Values profile to analyze regions of themolecule to assist in identifying areas for primers indifficult situations. Calculate Tm, GC and stability forprimers of a length specified and plot these profile values.
Use the Mutagenesis Profile to help construct mutant
primers, identify restriction enzyme sites that can be
introduced, or to check for changes in translation.

Organize, Use Primers•••

Design by positioning a primer in the molecule sequenceat a target position or just select (highlight) sequence inthe molecule viewer to initiate primer design at thisposition. View the primer evaluation, the sequence
flanking the primer, genes that are nearby, and the locationof neighboring primers that will meet the evaluation
criteria you have set.

Store primers in Primer Collections
Easy-to-use Create Product module
Use primer sites on molecule map

Store essential information about many primers in one ormore collection files for streamlined storage and access.
Create new collection files, as needed, and create folders
to organize your collection files.

Search in collection files to find a specific primer. Export
collection file data in tab-delimited format for use in otherapplications.

Use the Direct Entry wizard to enter sequence and otherinformation for primers already in use or purchasedcommercially. Use the Sequencing Primer Wizard todesign a set of primers for sequencing a molecule region.

Analyze Primers•••

Evaluate using primer criteria
Do in-depth analyses
Use the Analyze Mix Wizard

To find or evaluate primers, the program analyzes GCcontent, melting temperature (Tm), dimers, stability, runsof bases and repeats, hairpins and false priming. Detailed
analysis options display primer dimers, summarize
cautions, and report homologies between the primer andtemplate (false priming or other homologies).
The Analyze Mix Wizard will analyze primer binding andproducts formed in a mix of primers and molecules. Just
identify the primers and molecules, set the parameters forthe analysis, and view results.

Use the Create Product module to identify two primers andone molecule to produce an amplified product with a PCRtype reaction. Create a new DNA molecule or export theproduct sequence. Review product size, GC content,melting temperature, annealing temperature.

The Primer Viewer Window puts all primer information in
one convenient location. Click tabs at the bottom of thewindow to see primer information, edit the primer, oranalyze the primer. Save to a file or a primer collection.

Select a primer site on your molecule map and export theprimer sequence, rename the primer, create the primer
from its sequence, or (with a second primer on this map)
quickly create an amplified product.

Sci Ed Software LLC · www.scied.com

Email sales@scied.com·Phone (919) 386-1027

Align Multiple Sequences

Scan for Similarities•••••

Align many sequences against a reference
Align many sequences against each other
Save, export, edit alignment data

Scan sequence files in folders on your computer
Scan databank library files on your computer

Search for similarities to a sequence by scanning foldersof sequence files or databank library files on your personal
computer or local network. The program will open eachfile, scan the sequences found, and record significant
regions of similarity encountered. Set the speed and cutoff
value to alter the sensitivity of the search.

Align a group of DNA or protein sequences against areference sequence. View a summary table of results,aligned sequences in a variety of formats, or a graphic
display of areas of significant similarity in each sequence.
Enter name, description. Save alignment results.

Results include a sortable list or graphic view of regionsof similarity found, and aligned sequences or a detailed
map for each homology block listed. From the results list,
use the Scan Results Wizard to identify molecules to load
for use now, save to a disk file for later use, or set up as an
assembled multiple sequence alignment.

Sequence Assembly••

Simple or complex assembly projects
Locate subclones on reference sequence

Handles laboratory-sized assembly projects. Identify
sequence files to assemble and set assembly parameters, ifapplicable. Sequence assembly results are shown in a data
window with multiple views -- review a table of results
information, a picture view of alignment locations, or thealigned sequences with optional accessory data in a split
pane. Accessory data includes an assembly overview witha position locator, a histogram of coverage and errors, andtrace data, if available in the sequence files.

A multi-way alignment function lets you do exhaustive
pairwise alignments of all sequences and progressive
assembly of alignment using Neighbor-Joining phylogeny.
Alignment results include a dendrogram which suggests
the pattern of relatedness of all of the sequences aligned.
Edit alignment data — replace a base if you believe it is inerror, or shift unaligned bases left or right. If the sequence
files contain trace data, view the trace for a base inquestion before editing.
Export the consensus sequence derived from an alignmentor export the aligned sequences in CLUSTAL W multiple
sequence alignment format.

Compare Two Sequences•••

Find regions of local similarity
Progressively assemble an alignment
Layout of genomes showing conserved andrearranged regions

NCBI Blast Searches

Search two DNA or protein molecules for regions of local
similarity using the FastScan method, maximized for scoreor quality, or the Needleman-Wunsch method.

Initiate remote searches of NCBI BLAST databases, anddisplay results in a table format. The program helps you
set up a BLAST search by handling query sequence
formatting, in-frame translation, or excision of asubsequence. Pick the BLAST program and database touse and your request is sent to the NCBI server over theinternet. View BLAST results, access molecules of interestand save molecule files to disk or load a molecule for
immediate use.

Results of local alignments include a sortable list orgraphic view of similarities found, and aligned sequences
or a detailed map for each homology block listed.
Assembled alignments begin with a FastScan local
similarity search, lock in significant regions of homology
found, and then complete the alignment of the remaining

Sci Ed Software LLC · www.scied.com

Email sales@scied.com·Phone (919) 386-1027

Other Features

Analysis Functions•••••••

Integrated sequence editor and file handler
Extensive sequence formatting options
Use sequence phrase collections

Clone Manager reads files in GenBank, EMBL, FASTA orClone Manager file formats, or sequence data in simple
ASCII text files. You can also import (paste) files fromthe clipboard or retrieve files from Entrez (NCBI).

Open Reading Frame analysis
DNA Repeats, Dyad Symmetries analyses
Hydrophilicity, Protein structure analyses
Mutagenesis Profile moduleOpen Reading Frame analysis maps start and stop codons
in 6 reading frames and calculates Fickett's TESTCODE
scores to help identify coding regions.

The sequence editor can display full or partial sequences
in a variety of formats. Display any combination ofsequence, enzyme sites, sequence labels, translation,
annotations and memorize your favorite style settings.

Analyze direct or inverted repeats and dyad symmetries toidentify regions that might be associated with biologically
active sites such as control regions, transcription
terminator regions, or RNA processing sites.

You can also edit sequences, join sequences, rotate
circular molecules, invert or translate sequences, findOpen Reading Frames, or find regions in the sequence thatmatch or nearly match a search string.

Analyze protein or translated DNA for hydrophilicity andsurface exposure. Analyze protein structure for alphahelix, beta-sheet (extended), beta-turn, random coil states.
Mutagenesis Profile shows a portion of molecule sequencewith one frame of translation and enzyme sites. View
possible silent changes, find 'almost' enzyme sites, or view
base changes required to change from one amino acid toanother. Introduce a mutation and create a new molecule.

DataBook is a simple, built-in database to store andorganize information about your molecules. Automatic
data entry makes it really easy to use. Another module
stores sequence phrases in collection files and lets you findmatching sites in your molecules.

Sample Pricing and System Requirements
Recommended configuration: Windows 10 or 11. 64bit (x64) Windows. 40 Mb hard disk space required for program
installation. Internet connection required for license activation. Concurrent user license installation supports moststandard Windows network systems or TCP/IP networks. Upgrades from versions 9, 10 or 11 available.
Selected Pricing and License Type Examples

Price *Catalog No

Clone Manager Professional 12, single Seat License$800 USD

12-2523 Qty 1

Clone Manager Professional 12, 2 Seat Licenses$1280 USD

12-2523 Qty 2

Clone Manager Professional 12, 4 Seat Licenses$2140 USD

12-2523 Qty 4

Clone Manager Professional 12, Concurrent 2-User License$2050 USD

12-2524-2

Please visit our website, https://scied.com, for more detailed information about ordering, licensing and pricing.
January 2024. Prices subject to change without notice. * Plus applicable taxes.

License Information

Ordering Information

Seat License — Each seat license can be installed on asingle individual computer. License activation required.

Please view detailed ordering and licensing information at
our website, https://scied.com, and access links to make alicense purchase through our on-line reseller.

Concurrent User License — Install license service on asingle network server. Permits licensed number of users
to concurrently use the program.

Purchased software and evaluation (trial) programs can be
downloaded from our website. License serial numbers andactivation keys will be provided by email.

Our licenses are not term-limited and do not expire.

Please register your software so that we can provide
technical support and so that you can deactivate/reactivate
licenses when needed. Details at our website.

For Research Use Only — Not for use in diagnostic
procedures.

Sci Ed Software LLC · https://scied.com
Email sales@scied.com·Phone (919) 386-1027