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  • Find Homologous sequences in genomes of interest

    Hello,

    I have a gene of interest(GOI) identified from a patent application which indicates to be a gene isolated from Boechera species. I have around 15 sequences of the gene having varying levels of similarity ( until 70% ). I have regulatory sequences which are responsible for expressing the gene and I also have the protein/peptide sequences these gene sequences code for. My goal here is to see if this gene/protein is present in other plant species of interest of which some have published annotated genomes and some have just a draft assembly created internally.

    My first step was to do a simple blastp of the protein sequences to my genomes of interest. However I could not see any valuable hits. What should I do next? I would like to see if other genomes harbor this gene or atleast be able to prove that this gene is unique and is not found in other genomes.

  • #2
    Perhaps a pfam search on the protein domains might find homologies of interest.

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