Question

Finding a sequence

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2.4 years ago

Etienne • 0

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?

Thanks for advance!

SRA blast • 806 views

ADD COMMENT • link updated 2.4 years ago by shenwei356 8.4k • written 2.4 years ago by Etienne • 0

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Blast seems like your best bet, unless there's a specific type of sequence you'd like to search against

ADD REPLY • link 2.4 years ago by Jautis ▴ 530

score 2 · Answer 1 · 2021-12-06

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.