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IMC has various PCR Primer design methods.

The ability to simply drag the nucleotide sequence on the sequence lane and register it as a primer

• Register primers from the sequence lane
• Register primers from the feature lane

Ability to design features on the feature lane and primers to amplify inside and outside the selected area

• Primer design for amplifying included products, including selected features of feature lanes
• Primer design for amplifying the product containing or containing the selected genomic region of the feature lane

A function of designing primers that amplify a large number of areas at once (with Iterate Design function: it is a function to repeat the design until there is no area that can not be designed)

• Batch PCR Primer Design Batch PCR primer design to amplify all features with specified feature key on genome
• Whole Genome Covering PCR Primer Design PCR primer design that PCR product completely overlaps whole genome or large genomic region with PCR product overlapping
• Sequencing Primer Design PCR primer design for sequencing DNA fragments that can not be covered with one lead of a capillary sequencer
  reference

The following is a function to design a group of primers for cloning multiple DNA fragments at once, such as gene cluster design. From design to cloning, you can load cloned products into the IMC.

• In-Fusion Design Ver.1: Primer design function for In-Fusion Cloning
• In-Fusion Design & Build Ver.2: Primer design function for In-Fusion Cloning
• In-Fusion Design & Build Ver. 3: Ability to design and build gene clusters by dropping DNA fragments to be inserted into vector sequences
• Batch Gene Cluster Design & Build: the ability to design and build lumped numerous gene clusters by replacing the gene sets that make up the cluster
• Combinatorial Design & Build: The ability to combinatorially combine design and build a fragment constituting a gene cluster

Purpose and overview

• Ligation is an essential experiment to perform molecular cloning. IMC combines various nucleotide sequences including annotated nucleotide sequences with each other in the same manner as in actual cloning experiments to generate the products. All annotations are properly succeeded also to the ligation products and their products can be analyzed using many functions of the IMC as well as the original base sequence.

Function

• If the terminal sequences complementarily match each other, ligate them into one base sequence.
• Up to 5 fragment segments can be ligated.
• You can generate all possible ligation sequences.
  • In Version 7.24 and later, the complete complementary sequence of the ligation product is counted as a separate product.
• Annotated nucleotide sequences of GenBank and EMBL format can be ligated as well, and these annotations are properly inherited by the ligation products.
• If the shapes and sequences of the ends of the base sequence complementarily match, a circular base sequence is generated.
• It displays a list of restriction enzymes that can be used to check the insert direction of each fragment in the generated ligation product.
  • Also displays gel electrophoresis pattern when using these restriction enzymes.
• Displays the terminal shape of all base sequences loaded in the current folder.

• The base sequence generated as a ligation product can be analyzed in the same way as the original base sequence.

Restrictions

• Currently, ligation linking 6 or more base sequences is not possible.

Algorithm

• For restriction enzyme cleaved sequences on IMC, special Feature Keys and Qualifiers are generated that indicate the terminal status.