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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.
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.
Click "Tools -> Multiple GenBank File Expander" from the menu.
Load the closely related genome sequence (CDS must be annotated) to be compared into the current reference directory.
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.
This function is implemented in the following edition.
IMCDS
Extract the core genome from a pan genome.
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.
Load the base stock genome into the current main feature map.
Load multiple closely related genomes to compare with the current reference feature map.
Perform a homology search using Blast with the CDS feature included in the selected area of the feature lane of the main feature map as the query sequence.
Homology search results are recorded in the Qualifier of each feature.
These qualifiers can be displayed the features' shapes, colors, labels, etc accordingly.
I will inform those who are using IMC, GT with a floating license (dongle version).
If you upgrade the version of Jave to Jave 10, you can not use the dongle (Sentinel Hardware key).
We are currently considering countermeasures, but please use Java 8 as far as possible.
If you have already updated to Java 10, please contact us.