Genome Analysis Software Site

in silico biology, inc.

IMC L09A Color Presentation of CDSs categorized by COG code

  • 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.
  • 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.

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