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I have 500 M.Bovis isolates and I want to extract the rpoB and katG genes from these sequences. I took the nucleotide sequences from NCBI and saved them as a fasta file, and then tried to blast for one isolate using:

blastn -db databases/reference \ 
  -query sequences.fasta \
  -evalue 1e-3 \
  -word_size 11 \
  -outfmt 0 > sequences.reference.

But my output contains other quality data apart from the sequences. Is there anyway to extract just the sequences without other information?

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Thats easy simply use minimap

minimap2 --heap-sort=yes --splice-flank=no mygenomes.fastq.gz fastaDB.fas 

where

mygenomes.fastq.gz

is the 500 M. bovis genomes and ...

fastaDB.fas

are the genes you are interrogating the database with

The default parameters are set for the problem you are facing, i.e. to extract target genes within a species. In addition, you can just load fastaDB.fas with all the genes you are searching and it will loop through all of them on a single run.

It does have complex parameterisation, but thats usually to lower the criteria for a hit between the query sequence and genomes database.

minimap can ingest directly from a zip file (big advantage), has some parallelisation abilities (3 CPUs used) and its very fast (faster than Blast).

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    $\begingroup$ Appreciate the help $\endgroup$
    – user142632
    Commented May 28 at 3:46

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