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How do i search a FASTA database by sequence in seqkit?

Database: ribogrove_11.217_sequences.fasta (https://mbio.bas-net.by/cager/en/content/56-ribogrove#downloads)

Query sequence: sequence in .fasta file obtained from NCBI. (example: https://www.ncbi.nlm.nih.gov/nucleotide/NR_117620.1)

Iَ want it as: 100% identity matching but query sequence can be shorter/longer than those in the database.

seqkit rrna genomics 16s gene
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updated by GenoMax GenoMax • written by Mahmoud Reda • Mahmoud Reda

1 answer

You could do it using seqkit grep or locate but in this case you should use a proper search program like blat instead.

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written by GenoMax GenoMax

i got it

"seqkit locate --pattern-file seq.fasta ribogrove.fasta -o found.fasta"

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written by Mahmoud Reda • Mahmoud Reda

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