IMC Version Up History 7

Last Modified: 2019-02-06 (水) 22:41:06


7.30 2019/01/30

  1. In "Batch PCR Primer Design", a bug in which the function (Iterate Design) to repeatedly design the area that can not be designed with different conditions becomes an error has been fixed.
  2. Due to format change of multi GenBank file,  functions of "Multiple GenBank File Expander" is improved.
    • A function to skip the same error was added when confirming with error message.
    • A function to join individual header + feature files and base sequence of FASTA and expand it into a single GenBank format file has been added.
  3. The "Save the Layout Style as ..." button label in the "Feature Layout Style Setting" dialog has been changed to "Export Style (s) ...".
    • In addition, newly add "Save Layout File as ..." and save the whole layout file with the specified directory and file name.
    • This function is the opposite function of "Load Layout File ...".
    • In this list, the default style has been marked.
    • A new item is added to the list, and "Default Style" is displayed there.

7.29 2018/12/11

  1. In the CreateDB function, creation of a database for Blast search not only from GPFF but also from GBFF files is available.

7.28 2018/11/08

  1. The bug is fixed that the color setting dialog of Set Qualifier -> Color is not displayed on the right click menu on the feature
  2. Default Layout Style of Plasmid Map has been set.
  3. When drawing using Layout Style with Plasmid Map, write that information in the sequence file so that it can be rendered next time with that layout style.
  4. Fixed a problem that the dot fill color of DotPlot Navigation Dialog was rendered with blast color condition mismatch color.
  5. The problem that Show Grid Line can not be unchecked in the Sequence Lane tab pane of the Feature Setting dialog, has been resolved.
  6. The scale setting of the Sequence Lane tab pane of the Feature Setting dialog has moved to the Ruler for Sequence setting dialog of FLS.

7.27 2018/10/31

  1. E-Value, Overlap Length and Percent Identity have been added to the display items of the Binary Best Hit List dialog.
    • The Binary Best Hit List dialog is used in Gene Cluster Alignment and others.
  2. Conventional fixed license can be updated with new license authentication method.
    • With the new license authentication method, you can easily change the license between PCs at any time.
    • In the old method, it was necessary to switch requests with e-mails and to pass authentication files.

7.26 2018/08/28

  1. Menu has been changed
    • Genome Analysis -> Create -> Multiple Alignment to go to the upper menu, Genome Analysis -> Multiple Alignment.
    • Genome Analysis -> Create has been changed to Genome Analysis -> Feature Operation
    • Feature Fusion which was under Genome Analysis -> Create became Genome Analysis -> Feature Operation -> Feature Fusion with its name unchanged.
    • The Overlap Feature that was below Genome Analysis -> Create has been renamed to Genome Analysis -> Feature Operation -> Feature Operators.
  2. The problem of dongle driver installation from the IMC Setup DVD has been resolved.
  3. The stop codon absent region display of Frame Lane has also been changed to a method referring to Genetic Table.
    • Display stop codon absence area using the specified stop codon of Genetic Table.
  4. In the Settings -> Feature Settting -> Blast Color setting, it is now possible to set the filling color dedicated to the search result that passed through the condition filter without meeting the judgment condition.
  5. In Gene Cluster Alignment, the rendering of bands joining between homologous Features has been improved.
    • Bands are now drawn from outside the feature.

7.25 2018/08/22

  1. The bug that the position of the reference linear genome map does not move has been solved even if you drag and move the array node of the reference directory tree.
    • It has been changed to reference from the Genetic Table which specifies the start codon and stop codon used for ORF Extraction.
    • Formerly we have specified the stop codon directly.
  2. The display method of Gene Cluster Alignment has been improved.
    • The drawing color of the band that binds the homologous gene has been associated with Blast score color.

7.24 2018/08/14

  1. Up to 24 lanes can be displayed by restriction enzyme fragment gel electrophoresis of multiple samples.
    • You can change the number of lanes displayed on one page.
  2. The line between lines joining homologous genes of Gene Cluster Alignment has been changed to filling display.
    • It is not yet supported for printing and image output.
  3. Fixed bug that amino acid database can not be registered in setup from DVD.

7.23 Not Released

7.22 2018/08/03

  1. Multiple Trace Chart function has been improved.

7.21 2018/07/30

  1. Result in Global Genome Rearrangement Map Fixed an issue that rendering was distorted when Windows width was 950 pixels or less.
  2. Fixed a problem of "For input string error" when processing "Insert as New Feature" many SNPs at the same time in Mutation Search.
  3. The following notation was corrected.
    • "Search Pathway for ARM" in Sub Menu Item has been changed to "Search Pathway by ARM".
    • "Search without homology area" has been changed to "Show non homologous region" on the display on the execution dialog of Global Genome Rearrangement Map.

7.20 2018/07/30

  1. A. A. Mapping displayed a "For input string" M "error message has been resolved.

7.19 2018/07/27

  1. Mutation Search, the following improvements were made.
    • When selecting the resulting mutation point The corresponding base in the sequence lane of the main feature map is highlighted.
    • Display the base of the mutation in the corresponding position of the reference genome map.
    • Added the ability to register the mutation selected from the mutation displayed in the mutation list as a new feature.
      • In this case, describe the mutant base in the Qualifier / note = of Current File

7.18 2018/07/23

  1. A new menu item "Genome Design" has been added. Genome design related functions will move.
  2. Multiple lane gel electrophoresis can now be displayed when restriction enzyme digestion is performed for multiple genomic sequences.
  3. The specification of the return button of the execution dialog of Homology Search and Primer Design has been changed.

7.17 2018/07/15

  1. Time Limited License As the sale starts, the number of days until the license expiration date is now displayed.
    • Permanent license does not display correctly.

7.16 2018/07/12

  1. I changed the display on some dialogs.

7.15 2018/06/29

  1. An item has been added to the format of CSV output file of Mutation Analysis.
    • The gene name (gene) of the mutation site and locus_id have been added.

7.14 2018/05/31

  1. Mutation search function was added.
    • Select reference sequence in Genome Analysis menu → Compare → Mutation Search. .
    • Perform a homology search (blastp) on the reference sequence using the CDS of the current data as a query.
    • Bidirectionality is checked.
    • Alignment is performed with nucleic acid sequence of CDS of top hit.
    • Mutation points are searched.
    • The results are displayed.
    • Click the result to jump to the target position.
    • You can choose to distinguish between CDS and Intergenic region as the search scope.

7.13 2018/05/30

  1. A vertical line of different thickness was added to the shape of the feature key.
    • The thickness is 1-5 pixels.
    • It will be drawn at the center of the feature.
    • If you are divided by Join, such as exon, intron, etc., it will be drawn at the center of each join With + codon substitution function, in addition to all CDS batch processing, the function to process only the specified CDS has been added.
  2. Fixed a bug that caused an error when loading a fasta file or a genbank file without CDS in the reference genome and executing homology search. Fixed a bug in which primers designed with primers that span the circular genome (N, 1) are designed primers that can not amplify sequences that span N, 1.
    • The designed primer itself had no problem.
    • There was a bug in the position setting of the design result.
  3. Plasmid map Fixed a bug that features are not displayed if the conditions are met.

7.12 April 15th, 2018

  1. Bug # 2188: A bug in which values ​​larger than N are displayed when displaying feature position information that cross N, 1 has been resolved.
  2. Bug # 2189: The menus displayed by the right click of the specified range may be different may be solved.
  3. Spec # 2187: The function to search the optimal primer which amplifies the specified range from already registered primer was added.
  4. Spec # 2190: A function to replace CDS so that it is not disconnected by a specific restriction enzyme has been added.
    • Based on the specified codon frequency table, codons to be replaced are selected with high frequency of use.
    • The substituted codon is saved in Qualifier / modified_base =.
  5. Spec # 2186: Changed that LGRM automatically saves Multiple CSV file output.
    • In the past, a dialog was displayed at the end of the analysis and asked whether to save it or not.
    • After correction this time, it asked whether to save before execution, it was changed so that it will be automatically saved according to the specification at the time of execution, and finished.

7.11 February 21st, 2018

  1. Fixed a bug where mismatch list of LGR Map stays open even if cancellation of current array designation is canceled.
  2. A bug in which array names can not be copied or the current folder can not be moved by creating directory names similar to the same hierarchy has been fixed.
    • For example, if c: \ seq is the root directory and a directory called E. coli and E. col. O 157 is created under it, you can not copy the array from E. coli to E. coli O157 by drag & drop.
    • E. coli.O 157 can not be the current directory after making E. coli the current directory.
  3. A function to display the matching bases with Main reference genome on LGRM Multiple CSV file output has been added.

7.10 February 16th, 2018

  1. A bug that Primer Feature Position shifted by 1 base has been fixed.
    • When registering primers as features on the map with Insert New Feature, they were registered with a shift of one base.
  2. A function to sort file names of the directory tree has been added.
    • Right-click on the current directory → Sort Filename → Sort is performed in ascending / descending order.
    • Only the current directory can be sorted.

7.09 February 13th, 2018

  1. A bug that caused an error when executing LGRM has been fixed.
    • An error occurred when CDS existed at (N, 1) position.
  2. When copying from Main Current Folder to Reference Current Folder, the message when the same array already exists has been changed.

7.08 January 24th, 2018

  1. It is now possible to combine LGRM continuous execution and execution results.
  2. A bug in which the amino acid sequence display of LGRM is shifted has been fixed.

7.07 January 16th, 2018

  1. When LGRM runs it generates a copy of the underlying genomic sequence and LGRM runs on that copy. For this reason, the Lismal List of LGRM is kept on the copy side, and the LGRM Mismatch List Window is no longer displayed when reloading the original genomic sequence as in the past.
  2. A bug in which Frame Lane is not displayed has been fixed.
  3. DotPlot's XY ratio maintenance zoom can now be operated with the mouse wheel.

7.06 January 12th, 2018

  1. The following functions can be executed from "Codon Position List Window" which can be started from Codon Usage Window.
    • You can register the selected codon position as a new feature. At this time, you can select any feature key.
    • You can replace the selected codon with another codon (this codon must be registered as a feature in advance). In addition, in the feature - / note =, the codon before substitution is recorded.
  2. A header was added to the CSV file output from the Local Genome Rearrangement Map (LGRM).
  3. The problem that the Local Genome Rearrangement Map (LGRM) freezes during processing has been solved.
  4. When the intron is included in the CDS, the display position of the amino acid displayed in the sequence lane shifted (after the second exon) the problem was solved.

7.05 December 21st, 2017

  1. A bug that the display position on the reverse side is shifted by 1 base in the on sequence display of Feature has been fixed.

7.04 December 8th, 2017

  1. A window for displaying the list of its occurrence positions from each codon of Codon Usage Window has been added.
    Display items
    genome position, genename, Product etc.,
    • Clicking on one line in that list moves you to the appropriate position in the feature map.
    • Also at that time, highlight the corresponding codon in Sequence Lane.

7.03 December 6th, 2017

  1. A bug that prevented you from moving from the homology search results to the homology domain has been fixed.
    • Click on the list to move to the corresponding position and flip the homology area with a light blue color.

7.01 November 26th, 2017

  1. Multiple Exon CDS can now be registered directly from Frame Lane 's Stop Codon absent area (s).
  2. Cloning menu composition has been changed.
  3. A bug that freezes at the end of file loading has been resolved.
  4. The zoom out function has been improved.
  5. By selecting the Primer feature of the Feature Map, you can now register the primer by right clicking on the mouse.
  6. Feature Layout Style can be saved for each style.
  7. In the Search Unique Region function, clicking a list now displays the feature map of that position.
  8. The name of the button whose Default Style is currently used Feature Layout Style has been changed from "Default" to "Save the Style as Default".
  9. The default value of Outside Primer Search Range of Primer Design Parameter has been changed.
  10. Fixed a mistake in the unit of Primer Design Parameter.
  11. "Scope capture" has been added to the screen capture function.
  12. The auto generation serial number which conventionally generated too long name was shortened. It is automatically set to the number of consecutive serial number saved + number of files to be generated.
  13. The preservation and application function of Feature Setting foul which was difficult to understand in the past was improved.
  14. You can now specify all feature keys on sequence lane display.
  15. Fixed a bug that could not capture the window on subdisplay when using extended discussion.
  16. Conventionally, the IMC Version name, which was represented by three numerical values, such as 6.0.44, has been changed to two numerical expressions, such as 7.01.
  17. We unveiled a tool group that was not officially released.

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Last-modified: 2019-02-06 (水) 22:41:06 (162d)