Genome Analysis Software Info Site

Although macOS 11 Big Sur has been released, the following problems have been reported regarding our products when the version is upgraded to the OS.

1. The dongle does not work properly. The Corresponding Dongle Driver has not released from the maker yet.

The workaround is either of the following.

1. Revert to macOS 10.
2. Switch from dongle license to activation license (free of charge). Please contact us.

• CDS candidates can be registered as new features from the stop lane stop absence region of the frame lane.
• This is not a CDS prediction function. The GT-AG rule is ignored.

Operation

Phenomenon

In Frame Lane, if you select a region where the stop codon does not appear and register that region as a new feature by right-clicking the mouse, that region will be complemented in the Description Window even though it is in Forward Strand.However, it occurs in the case of new registration from the 3rd frame of Forward Strand. Registration from the 1st and 2nd frames works normally.

Immediate countermeasures

Uncheck Complement in the Description Window and register.

Counter-measure

Bug fix Version IMC Ver.7.46 has been released (2020/12/09).

Phenomenon

• The LED of the dongle is lit, but the license is not recognized, the "License request" dialog is displayed, and IMC cannot be started.

Cause

• Due to the recent Java Version Up, activation may not work properly.

Coping

• Reverts the Java version to the previous version.
• If you cannot change the Java version to the previous version, please contact in silico biology, inc. Temporarily issue a fixed license.

Extract the GBFF file consisting of many single GanBank format files into a tree-like directory according to the Taxonomy description of each GenBank file and place it in IMC so that it can be handled easily.

Background

The sequence data of GenBank and RefSeq are compiled into a large compressed file at each release time.

Each entry consists of a header file (*. Gbff) and an array part (* fna). In order to make a single GenBank file, it is necessary to combine these two kinds of files.

GenBank File Expander decompresses these files of GenBank and RefSeq, synthesizes them, and unfolds them as a phylogenetic tree-like directory in an arbitrary place.

If you specify this expanded directory as IMC's root directory, it can be displayed and loaded in IMC's directory tree.

Operation

Click "Tools -> Multiple GenBank File Expander" from the menu.

To rebuild the designed gene cluster, fragment the cluster optimally.

After each fragment is chemically synthesized, each fragment is reconstituted by OGAB method to prepare a long chain DNA cluster.

Implementation Edition

This function is implemented in the following edition.

IMCDS

Operation

Extract the core genome from a pan genome.

Preparation

Load one genome into the current main feature map.

Load multiple genomes to compare to the current reference feature map.

Detects one base mutation between closely related genomes and generates a list of all mutations. In addition, from the list you can display the variation of the reference feature map and the base position of the corresponding main feature map.

Preparation

Load the base stock genome into the current main feature map.

Load multiple closely related genomes to compare with the current reference feature map.