This is a method to automatically generate the genome of a closely related species as a reference database for Blast search.
Menu: File-> Load Sequence Files to Reference…
- Load the genome (annotated) of the closely related species into the Reference Directory.
- Two types of Blast search databases are automatically generated when loading is completed.
- Generates the base sequence of the entire genome as a nucleic acid DB.
- Generated as an amino acid DB with each amino acid sequence of all CDSs as an entry.
The following is a batch compatibility search method using the above.
Menu: File-> Load Sequence File (s)
- Loads the unannotated genomic sequence into the Main Directory.
- If the loaded genomic base sequence is divided into multiple contigs, it is convenient to use the Join function to virtually create a single sequence. (See here for the Join function)
Menu: Analysis-> ORF Finder-> ORF Extraction…
- Perform ORF extraction on the unannotated genomic sequence that has been combined into one.
- Check Only longest ORFs are extracted….
- If the Search Range is highlighted in red, only part of the genome sequence is selected. If you want to analyze the total length, you need to change From To to specify the total length.
- When the ORF extraction is finished, the extracted ORF will be displayed on the main feature map.
- (There is also a method of mapping the gene identification result to the base sequence)
Menu: Analysis-> ORF Finder-> Translation
- Translation is performed on the result of ORF extraction.
- If you need to change the Codon Table, change its number
- When it finishes running, the ORF feature changes to a CDS feature.
Menu: Analysis-> Homology Search for Selected Feature Key
- Perform an homology search on the closely related genome loaded as the reference genome for each unannotated CDS on the amino acid-translated main feature map, automatically extract annotations from the hit subjects, and annotate. I will do it.
(Menu: Settings-> Feature Setting .. TAB: Auto Copy)
- (Use Feature Setting to fine-tune which information on the reference genome is extracted)
- When the execution is finished, the hit information is posted and annotated.
Menu: File-> Save as…
- Save the annotated file with a different name to save the results.
- (The result is automatically saved even if you do not save the file, but if you execute other analyzes repeatedly, it will be mixed with the result of the homology analysis.)