Last updated:2015.12.25.

UME User’s manual


 

What is UME?

UME (Utilities for MSS file Error check) is a stand-alone tool to check syntax and format of Sequence file and Annotation file required for using Mass Submission System (MSS) of DDBJ.
UME does not have any function to make Sequence file or Annotation file for your submission. So, please make your submission files by using text editor, spreadsheet software, or some application in your PC, appropriately. To make both Sequence file and Annotation file, please read Making MSS Files.
Before using this software, please confirm End-user license agreement, carefully.

Basic function

The basic functions of UME are followings.

Parser
You can verify the syntax and format of Sequence file and Annotation file.
transChecker
If your data include CDS features (protein-coding sequence), you can validate the amino acid translation.
FFconv
By using FFconv, you can make simulated format of DDBJ flat file from Sequence file and Annotation file.
AGPParser
For the submission of contig (CON entries), AGP file and Annotation file by AGPParser.

Install

Before installing UME, see End-user license agreement and System_requirements.
Please Install UME.

 

Broad overview

Starting UME

You can run UME application by double clicking the UME icon (Depending on your PC environment, some extension of UME file would be displayed) in the UME folder.

 lib folder
Directory which includes library files used by UME. If you move this directory or any file in it, UME would not properly work.
 resource folder
Directory which includes resource files used by UME. If you move this directory or any file in it, UME would not properly work.
 sample folder
Including sample files for DDBJ submission.
 UME file
Start UME application by double-clicking this file.
 license file
A text file for license agreement. Please read at first.
The contents of the file are the same as End-user license agreement.

 

Initial setting of UME

At the first time, you run UME application, change the maximum size of RAM for UME to optimize run-time environments. The default configuration of it is 512 Mbytes.

  • (1) Click Config in menu bar.
  • (2) Select the appropriate size of Max memory for runtime from pull-down menu.

 

Framework of each panel

Check panel: basic verification of submission files

You can move to this panel by clicking the Check tab enclosed in the red square. See also section Basic verification of submission files.

  • (1) Specify the subjects, both Annotation file and Sequence file.
  • (2) By clicking Execute button, verify the files specified at step (1) by Parser.
  • (3) By clicking Execute button, validate amino acid translation of the files specified at step (1) by transChecker.
  • (4) By clicking Execute button, process the files specified at step (1) by FFconv.
  • (5) By clicking Exit button, Close UME.

 

Contig panel: verification of AGP file for contig submission

You can move to this panel by clicking the Contig tab enclosed in the red square.

  • (1) Specify the subject, Annotation file.
  • (2) Specify the subject, AGP file.
  • (3) Specify the subject, Multi-fasta file for components in AGP file.
  • (4) By clicking Execute button, process the files specified at steps (1) to (3) by AGPParser.
  • (5) By clicking Exit button, Close UME.

 

Basic verification of submission files

After preparing Annotation file and Sequence file, please verify them by using Parser before sending them to DDBJ.
If your data include CDS features (protein-coding sequence), please validate translated amino acid sequences by using transChecker.
If you find some error messages please correct them, appropriately.

 

Parser: verification of syntax and format

Execute Parser through the following steps.

Click Check tab and move to Check panel.

  • (1) Specify the subjects, both Annotation file and Sequence file.
  • (2) By clicking Execute button, process the files specified at step (1) by Parser.
  • (3) When you check the box, Save log in file, the result log of Parser is saved as a text file.
  • (4) The window of Parser log is opened.
  • (5) The progress of Parser is indicated.
  • (6) The result log of Parser is displayed.
  • (7) By clicking Save button, the contents of (6) are saved as a text file.
  • (8) By clicking Close button, the window, Parser result, is closed.

To understand meanings and solutions of Parser error messages, see Format of Parser outputs and List of Parser error messages.

 

transChecker: validation of amino acid translation

transChecker can translate nucleotide sequences of Sequence file into amino acid sequences corresponding to CDS features specified at Annotation file.
Before using transChecker, both two files should be checked by Parser, and remove all of Parser errors.
Please note that when some Parser error is found, transChecker is terminated without any result.
Execute transChecker through the following steps.

Click Check tab to move to Check panel.

  • (1) Specify the subjects, both Annotation file and Sequence file.
  • (2) By clicking Execute button, process the files specified at step (1) by transChecker.
  • (3) When you check the box, Save log in file, the execution log and error messages of transChecker are saved as a text file.
  • (4) When you check the box, Save translated sequences in file, the amino acid sequences translated by transChecker are saved as a text file in either of two formats.
    You can specify the format for translated amino acid sequences from following two types;

  • (5) The window of transChecker result is opened.
  • (6) The progress of transChecker is indicated.
  • (7) The execution log and error messages of transChecker are displayed.
  • (8) By clicking Save button, the contents of (7) are saved as a text file.
  • (9) The amino acid sequences translated by transChecker are displayed in the format selected at (4).
  • (10) By clicking Save button, the contents of (9) are saved as a text file.
  • (11) By clicking Close button, the window, transChecker result, is closed.

To understand meanings and solutions of transChecker error messages, see Format of transChecker error messages and List of transChecker error messages.

 

FFconv: confirmation by making simulated DDBJ flat file

FFconv can make simulated format of DDBJ flat file from Annotation file and Sequence file.
Before using FFconv, both two files should be checked by Parser, and remove all of Parser errors. Please note that when some Parser error is found, FFconv is terminated without any result.
Execute FFconv through the following steps.

Click Check tab to move to Check panel.

  • (1) Specify the subjects, both Annotation file and Sequence file.
  • (2) By clicking Execute button, make simulated format of DDBJ flat file from the files specified at step (1) by FFconv.
  • (3) When you check the box, Save flat file in file, the result of FFconv, simulated format of DDBJ flat file, is saved as a text file.
  • (4) The window of FFconv result is opened.
  • (5) The progress of FFconv is indicated.
  • (6) The execution log of FFconv is displayed.
  • (7) By clicking Save button, the contents of (6) are saved as a text file.
  • (8) The result of FFconv, simulated format of DDBJ flat file, is displayed.
  • (9) By clicking Save button, the contents of (8) are saved as a text file.
  • (10) By clicking Close button, the window, FFconv result, is closed.

 

AGPParser: verification of AGP file for contig submission

Many genome projects submitting a lot of HTG and/or WGS entries can often provide the information to assemble a series of their entries and reconstruct a genome structure. An accession number would be assigned for such contig tiling path, and call it Contig (CON) entry, which is classified into CON division. CON entry has the CONTIG line that indicate accession numbers of cited sequences (piece entries) and their tiling order to construct the contig. The nucleotide sequence of CON entry is not shown on DDBJ flat file.

DDBJ can NOT directly accept the submission of CON entry.
At first, you have to submit all piece entries to construct the contig, then a CON entry will be constructed. APG file is required to submit a CON entry.

For the submission of CON entry, please read Making MSS Files.

Executing AGPParser

Basically, AGPParser checks the format of AGP file. When you specify Annotation file and/or multi-fasta file including all of sequences cited by AGP file, AGPParser also checks the consistency between the two or three files.

Click Contig tab to move to Contig panel.

  • (1) Specify the subject, Annotation file. Not required.
  • (2) Specify the subject, AGP file. Required.
  • (3) Specify the subject, the multi-fasta file including all of sequences cited by AGP file. Not required.
  • (4) By clicking Execute button, AGPParser checks the specified file at the steps (1) to (3).
  • (5) When you check the box, Construct sequence from AGP and multi-fasta files, AGPParser constructs a text file for nucleotide sequence(s) on accordance with the specification of the two files.
  • (6) Check the button, Save log in file, then the result log of AGPParser is saved as a text file.
  • (7) The window of AGPParser log is opened.
  • (8) The progress of AGPParser is indicated.
  • (9) The result log of AGPParser is displayed.
  • (10) By clicking Save button, the contents of (9) are saved as a text file.
  • (11) By clicking Close button, the window of AGPParser log is closed.

Format of AGPParser error messages

When some error messages are found, it is required to correct and to fix them.
If you have any problems and/or questions, please contact us with error messages.

[Code Number]:[Level]:[Region]:[Body Text] or [Code Number]:[Level]:[Body Text]

Code Number; Indicate the code number of the message

Level; Indicate the level of the message;

  • FAT; Fatal error, related to system environment.
  • ER1; Type 1 error of the file format. Correction is required.
  • ER2; Type 2 error of the file format. Correction is required.
  • WAR; Warning for the file format. Correction is sometimes required.

Region; Indicate the region of the error as line number or object name

Body text; Detail descriptions of the message

List of AGPParser error messages

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