Restriction site analysis

You can search any restriction site on a DNA sequence. DNAMAN supplies two restriction enzyme files; the restrict.enz file with 180 most frequently used restriction enzymes, and the dnamanre.enz file with 1364 enzyme records. You can also create your own enzyme files. All the enzyme files are editable and expandable.

DNAMAN provides custom restriction enzyme filters on cutter, ends, frequency and methylation sensitivity. Users can define the DNA molecule as a linear or a circular type.

 

DNAMAN reports the restriction analysis results in an easy-to-read table. The cutting sites are shown in alphabetical order of enzymes, and in site position order as well. The non-cutting enzymes are also listed. In addition, DNAMAN displays enzyme sites on the top of the DNA sequence.

Restriction map

DNAMAN provides easy-to-use tools to produce publication-quality restriction maps. These tools can be used to draw linear or circular restriction maps with or without DNA sequence information. You can also draw maps for other projects, such as PCR strategy diagrams, gene structural maps, etc.

 

Restriction pattern illustration

DNAMAN predicts the patterns of restriction enzyme digested DNA fragments in a gel electrophoresis. You can perform single enzyme digestion on multiple sequences, and single or multiple digestion on a single sequence. DNAMAN shows the information of restriction fragments on their sizes and ends when you click on these fragments.

Electronic cloning

DNA cloning is a time consuming and expensive process. DNAMAN provides easy-to-use tools to design a cloning strategy and performs evaluation analyses on target sequences. This feature could improve the efficiency of your cloning work in laboratory.

DNAMAN mimics basic steps of the actual cloning process:

• Restriction analysis on the original vector and insert sequences
• Selection of vector and insert fragments from restriction pattern
• Verification of the end compatibility of DNA fragments
• Modification of fragment ends if necessary
• Insertion of linkers if necessary
• Producing the final clone sequence

Constructing restriction maps

DNAMAN can help you reconstruct a restriction map in the absence of DNA sequence. You must provide all fragment sizes in single and double digestion. DNAMAN deduces the possible restriction map(s) from the information of restriction fragments.

Silent mutation analysis

Silent mutation analysis allows you to design a desired mutation site on a DNA sequence. This mutation will result in the modification of restriction property without changing the coding amino acid sequence. This function searches for potential mutation positions to create or destroy restriction enzyme sites.

Directed mismatch analysis

Directed mismatch analysis allows you to create or remove restriction sites on a DNA sequence or its mutants (variants) by incorporating a single or double mismatch at a site near the mutation. Using this function you can create or destroy a restriction site in order to distinguish the wild type allele and a common mutant allele.