Answers.Body: <p>Thats easy simply use <em>minimap</em></p>
  <pre><code>minimap2 --heap-sort=yes --splice-flank=no mygenomes.fastq.gz fastaDB.fas 
  </code></pre>
  <p>where</p>
  <blockquote>
  <p>mygenomes.fastq.gz</p>
  </blockquote>
  <p>is the 500 <em>M. bovis</em> genomes and ...</p>
  <blockquote>
  <p>fastaDB.fas</p>
  </blockquote>
  <p>are the genes you are interrogating the database with</p>
  <p>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.</p>
  <p>It does have complex parameterisation, but thats usually to lower the criteria for a hit between the query sequence and genomes database.</p>
  <p><em>minimap</em> can ingest directly from a zip file (big advantage), has some parallelisation abilities (3 CPUs used) and its very fast (faster than Blast).</p>
  
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Answers.Text: Appreciate the help
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Body: <p>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:</p>
  <pre><code>blastn -db databases/reference \ 
    -query sequences.fasta \
    -evalue 1e-3 \
    -word_size 11 \
    -outfmt 0 &gt; sequences.reference.
  </code></pre>
  <p>But my output contains other quality data apart from the sequences. Is there anyway to extract just the sequences without other information?</p>
  
Tags: <blastn>
Title: Extract gene sequences from isolates
ThreadText: # Extract gene sequences from isolates
  
  (Asked by: username_0 on 2024-05-28)
  
  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?
  
  **Tags:** blastn
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2024-05-28. Score: 1 | Accepted answer
  
  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).
  
  > **Comments:**
  > **username_0**: Appreciate the help  
  
  ---
  
  