text: user3848: Is there a sequence format allowing multiple sequences to be grouped  across a flat file? The specific application is stacking separate nucleotide sequences against a given RNA secondary structure.
  To rephrase the same question I'm looking to stack viral nucleotide data in different groups across a single flat file. FastaQ provides an example:
  Traditional fastQ,
  @sequence_name
  AGCTGAT
  +
  ...(quality score)
  
  @sequence2
  AGCTGAC
  +
  ...(quality score)
  
  What I'm looking for is a format,
  @Gp1_virus1-2-3
  AGACGTAG
  +
  AGAGACAA
  +
  AGAGACAT
  
  @Gp2_virus1-2
  AGATGTAG
  +
  AGATACAA
  
  In the above example there are two groups comprising 3 (group 1) and 2 (group 2)  individual sequences (viruses). Here 'group' represents different structures.
  Stockholme format has potential. My understanding of this format, which is basic, is it stacks a sequence, together with structural information. What is sought is stacking multiple sequences and then a structure format. Any clarification would help.
  There are multiple XML formats, which may be relevant.
  Just to mention a 'flat file' is needed to allow manual inspection. Dumping JSON is a solution, but isn't friendly for optical inspection.
  
  Application
  The immediate downstream application is structure/sequence viewers. I think at least one. viewer will accept Stockholme 1.0 format. rFAM is very similar (@terdon's comment)
  Summarised Question The question could be rephrased as to whether multiple RNA families can be stacked inside one Stockholme 1.0 or else rFAM format?
  Some of the members here are likely familiar with pFAM. So could multiple protein structures be stored and retrieved inside one pFAM file.
  @gringer's contribution is very welcome.
  
  user73: An unmapped SAM file format allows for read groups. You can use samtools import to create unmapped SAM files from FASTQ files:
  samtools import -R virus-1-2 in12.fq > 12_reads.sam
  samtools import -R virus-1-2-3 in123.fq > 123_reads.sam
  samtools merge out.sam 12_reads.sam 123_reads.sam
  
  
original_text: 3848: <p>Is there a sequence format allowing multiple sequences to be grouped  across a flat file? The specific application is stacking separate nucleotide sequences against a given RNA secondary structure.</p>
  <p>To rephrase the same question I'm looking to stack viral nucleotide data in different groups across a single flat file. FastaQ provides an example:</p>
  <p>Traditional fastQ,</p>
  <pre><code>@sequence_name
  AGCTGAT
  +
  ...(quality score)
  
  @sequence2
  AGCTGAC
  +
  ...(quality score)
  </code></pre>
  <p>What I'm looking for is a format,</p>
  <pre><code>@Gp1_virus1-2-3
  AGACGTAG
  +
  AGAGACAA
  +
  AGAGACAT
  
  @Gp2_virus1-2
  AGATGTAG
  +
  AGATACAA
  </code></pre>
  <p>In the above example there are two groups comprising 3 (group 1) and 2 (group 2)  individual sequences (viruses). Here 'group' represents different structures.</p>
  <p>Stockholme format has potential. My understanding of this format, which is basic, is it stacks a sequence, together with structural information. What is sought is stacking multiple sequences and then a structure format. Any clarification would help.</p>
  <p>There are multiple XML formats, which may be relevant.</p>
  <p>Just to mention a 'flat file' is needed to allow manual inspection. Dumping JSON is a solution, but isn't friendly for optical inspection.</p>
  <hr />
  <p><strong>Application</strong>
  The immediate downstream application is structure/sequence viewers. I think at least one. viewer will accept Stockholme 1.0 format. rFAM is very similar (@terdon's comment)</p>
  <p><strong>Summarised Question</strong> The question could be rephrased as to whether multiple RNA families can be stacked inside one Stockholme 1.0 or else rFAM format?</p>
  <p>Some of the members here are likely familiar with <strong>pFAM</strong>. So could multiple protein structures be stored and retrieved inside one <strong>pFAM</strong> file.</p>
  <p>@gringer's contribution is very welcome.</p>
   73: <p>An unmapped SAM file format allows for read groups. You can use <code>samtools import</code> to create unmapped SAM files from FASTQ files:</p>
  <pre><code>samtools import -R virus-1-2 in12.fq &gt; 12_reads.sam
  samtools import -R virus-1-2-3 in123.fq &gt; 123_reads.sam
  samtools merge out.sam 12_reads.sam 123_reads.sam
  </code></pre>
  