Hi, I have a sequence from ITS1 (MT895507, Genbank acess) and I need to finding similares sequences in other works. My goal is to find how many sequences are similar to mine in that other work (PRJNA335788).
I was doing blast the SRA with my sequence of interest, but I don't know if that's correct. Please, could you help me?
If you want to search a sequence against a large number of sequences data, check the BIGSI or COBS, the latter is easy to install and use in a local machine. I've also developed a similar but faster one, will be open-source soon.
Since the PRJNA335788 has only 10 FASTQ files, you can also mapping them against the query sequence (534bp) in single-end mode using bwa or bowtie2. It should be very fast.