Genome Analysis Software Info Site

• Perform a homology search with COG, which is an ortholog database, on the genomic base sequence for which CDS has been identified, and automatically post the COG function classification code. As a result, each CDS can be displayed in color classification on the feature map.

Implemented Edition

• IMC GE, AE, DS, GT

Preparation

• COG database myva
• Genomic sequence file: for example Bsub 50 kb.gbk
• Although it can be executed with any genomic sequence, the eukaryotic genome sequence is not suitable as the COG database does not contain prokaryotic species other than yeast.
• The sample sequence is taken from a partial region of B. subtilis, but if it is executed in the whole genome, processing time may be required.

Operation

• Download the COG database.
  
  • It can be downloaded from NCBI or from our site download menu.
• Register the COG database.
  
  • Use the DB registration function for batch homology search.
• Select "File" -> "Create Blast DB" in Menu. Alternatively, click Create Blast DB in the toolbox.
  
  • Detailed information on "Create Blast DB" function
• Load genome sequence.
• The sample genomic sequence is generated in the "Users / Documents / sample" folder during IMC installation.
• Or you can download from our download menu.
• Execute ORF Extraction.
• Select "Genome Analysis" -> "ORF" -> "ORF Extraction ..." from the menu.
• 
• Perform amino acid translation, convert each ORF candidate to CDS, and at the same time perform that amino acid translation.
• Select "Genome Analysis" -> "ORF" -> "Translation" from the menu.
• 
• The Translation Run dialog is displayed.
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• If no amino acid sequence is registered in each CDS, the search will be "No Hit".
• This process is unnecessary if the amino acid sequence has already been registered in each CDS.
• Each ORF candidate is converted to CDS and amino acid translated using the specified Genetic Table.
• 
• Detailed information on amino acid translation function of CDS
• Perform batch homology search.
• To target all CDSs on the genome, select "Genome Analysis" -> "Homology Search" -> "Homology Search for Selected Feature Key" in the Menu or click the Bat Homology Search button in the tool box.
• 
• If you want to target all CDSs in a specified area on the genome, drag the area with the mouse and specify the area. Right-click on the selection area and select "Homology Search by
• Selected Feature" from the displayed pop-up menu.
• In the Batch Homology Search dialog that appears, select the COG database and click the Set button to start execution.
• Detailed information on Batch Homology Search function
• Classification code is displayed by Classification Code.
• Click the "Draw Feature in Classification Color" button on Toolbox.
•