Genome Analysis Software Site

in silico biology, inc.

IMC E04A2 Blast Search with Main Feature Query on Reference Genomes

  • In addition to directly entering the query sequence described in E04A1, by right-clicking the mouse on the feature displayed on the main feature map or the reference feature map, the sequence of the feature (base sequence, CDS etc. If it is, you can also execute Blast search with query sequence as amino acid sequence).
  • In this search, you can display maps near the features of hit subjects and query arrays automatically, and show them to align homology regions.
  • The query sequence can be a nucleotide sequence of a region selected by dragging on the main feature map and a feature on the main feature map or a nucleotide sequence or amino acid sequence of a feature present in the region and a reference genome It is the base sequence or amino acid sequence of any feature displayed on the map.
  • The database to be searched is the genomic base sequence of the reference genome map and the translated amino acid sequence such as the CDS feature when a feature or area on the main feature map is used as a query sequence.
  • When a base sequence or amino acid sequence of a feature on a reference genome map is used as a query sequence, it is an amino acid sequence belonging to the genomic base sequence and the CDS feature under the current main directory.
  • Perform a Blast search on the genomic base sequence and amino acid sequence on the current reference directory, with one feature on the main feature map as the query sequence.

Preparation

  • Load some closely related genomic base sequence files in the current main directory.
  • Load several related species genomic base sequence files in the current reference directory.
  • (In IMCEE and IMCSE, only one genomic base sequence currently displayed in the reference genome map is covered.

Operations

  1. Right-click on one CDS feature on the main feature map.
  2. The menu will be displayed. Select Show Homology -> Show Homology AA from that menu.
  3. A confirmation message "Start Homology Search?" Is displayed.
  4. Click "Yes (Y)".
  5. Homology search execution starts. A progress message is displayed during execution.
  6. When the search is completed, the "Homology Search" result dialog is displayed.
  7. Various operations are possible from this dialog.
  8. Since the number of hit entries for each database defaults to 1, the list only shows hits for the number of arrays loaded in the current reference directory.
  9. If you want to display not only the top hit but also the hit entry of the next point, re-execute the search and click "Show Parameter ..." to display the parameter and set "Maximum Number of Hits", " -num_descriptions "and" -num_alignment "to 2, respectively.
  10. The number of hits displayed does not necessarily correspond to the above numbers.
  11. According to other criteria, if there are no hits that satisfy the condition, it will be displayed less than the specified number.
  12. Click one line in the hit entry list. Click one line in the hit entry list.
  13. Then, the features of the query feature on the main feature map and the hit entries of the reference map are highlighted, and each feature lane is shifted and juxtaposed.
  14. Similarly, as you click on another line, homologous features on each genome sequence of the reference map map are juxtaposed.
  15. Check any hit entries.
  16. Click "Multiple Alignment ...". Click "Multiple Alignment ...".
  17. A confirmation message "Start Multiple Alignment?" Is displayed.
  18. The "Multiple Alignment" dialog is displayed.
  19. Molecular phylogenetic trees can also be drawn from this "Multiple Alignment" dialog.
  20. Click "Phylogenetic Tree".
  21.  

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