I have got a DNA-seq paired end dataset (fastaq). Would anyone please tell me how I should search for homologs of my gene sequence in this dataset?
I think I need to first convert fastq format file to fasta and then use blat. Would it be OK?
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I want to confirm that the homolog of my gene from species A (query) exists in species B genome (subject). Species A and species B are closely related species (the sequence similarity is expected to be 70% at the DNA level). Now there is no whole genome sequence available in species B. So the DNA seq reads are the only materials that I can use. Besides, will it be possible to get (or assemble) the full length of the homolog in species B?