Genome Analysis Software Info Site

This is a method to automatically generate a reference database for Blast searches from genomes of related species.

Menu: File -> Load Sequence Files to Reference…

• Load the genomes (annotated) of related species into the Reference Directory.
• When loading is complete, two types of databases for Blast searches are automatically generated.
• Generate the base sequence of the entire genome as a nucleic acid DB.
• Generate an amino acid DB with each entry for the amino acid sequence of all CDS.

The following is a method for bulk affinity search using the above.

Menu: File -> Load Sequence File(s)

• Load unannotated genome base sequences into the Main Directory.
• If the loaded genome base sequence is divided into multiple contigs, it is convenient to use the Join function to virtually combine them into a single sequence. (See here for the Join function)

Menu: Analysis -> ORF Finder -> ORF Extraction…

• Perform ORF extraction on the unannotated genome base sequences that have been combined into a single sequence.
• Check Only longest ORFs are extracted….
• If the Search Range is highlighted in red, only a portion of the genome sequence is selected. If you want to analyze the entire length, you need to change From To to specify the entire length.
• When ORF extraction is complete, the extracted ORFs will be displayed on the main feature map.
• (You can also map gene identification results to the base sequence.)

Menu: Analysis -> ORF Finder -> Translation

• Translate the results of ORF extraction.
• If you need to change the codon table, change the number.
• When execution is complete, the ORF feature will change to a CDS feature.

Menu: Analysis -> Homology Search for Selected Feature Key

• For each unannotated CDS on the amino acid translated main feature map, a homology search is performed against the closely related genome loaded as the reference genome, and annotations are automatically extracted from the hit subjects and annotation is performed.

(Menu: Settings -> Feature Setting.. TAB: Auto Copy)

• (Use Feature Setting to set in detail which information on the reference genome is extracted)
• When execution is complete, the hit information is transcribed and annotated.

Menu: File -> Save as…

• To save the results, save the annotated file under a different name.
• (The results are automatically saved even if the file is not saved, but if you run other analyses over the same time, they will be mixed with the results of the homology analysis.)