text: user2026: I am trying to recreate the experiment from Convergence of retrotransposons in
  oomycetes and plants by Kirill Ustyantsev, Alexandr Blinov and Georgy Smyshlyaev. In the "Methods" section a 
  
  HMM profile was constructed from the amino acid alignment of aRNH
    sequences from the Ustyantsev et al
  
  I was wondering where I could get this profile. I checked the cited papers but they were also referencing other papers. Could someone maybe clarify where I could get the profile?
  
  user298: The alignment they used to build the HMM is included as supplementary file 8 in the paper you cite:
  
  Multiple amino acid sequence alignment of RNH genes and domains from diverse taxa constructed and used for the phylogenetic reconstruction in the present study. (TXT 45 kb)
  
  So, you can download that alignment and then use a tool like hmmbuild (part of HMMER) to build the HMM profile:
  hmmbuild model.hmm 13100_2017_87_MOESM8_ESM.txt 
  
  The command above will create the file model.hmm which contains the HMM built from the alignment in the supplementary file 13100_2017_87_MOESM8_ESM.txt. I am including the first few lines here (this is not the entire file, don't use this as the model—build it yourself. I only include it to illustrate the format): 
  HMMER3/f [3.1b2 | February 2015]
  NAME  13100_2017_87_MOESM8_ESM
  LENG  121
  ALPH  amino
  RF    no
  MM    no
  CONS  yes
  CS    no
  MAP   yes
  DATE  Mon Dec 11 13:33:29 2017
  NSEQ  165
  EFFN  5.697556
  CKSUM 2893352190
  STATS LOCAL MSV       -9.8975  0.71332
  STATS LOCAL VITERBI  -10.6450  0.71332
  STATS LOCAL FORWARD   -3.9247  0.71332
  HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y   
              m->m     m->i     m->d     i->m     i->i     d->m     d->d
    COMPO   2.34473  4.21240  2.85435  2.69203  3.54228  2.79153  3.54812  3.01140  2.72630  2.48370  3.82225  2.94269  3.49156  3.05882  2.84632  2.63343  2.86306  2.72633  4.27012  3.56181
            2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
            0.13773  5.45955  2.08419  0.61958  0.77255  0.00000        *
        1   2.99488  4.57852  4.44659  3.29307  1.80597  4.16203  3.88788  2.87265  3.75733  2.38594  3.30344  3.33633  4.53284  3.64324  3.69630  2.90350  3.30742  2.83413  4.36991  1.50673      1 y - - -
            2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
            0.00723  5.32905  6.05140  0.61958  0.77255  0.45275  1.01027
        2   2.66602  2.17750  5.01715  4.40788  1.72617  4.29647  4.62737  2.89579  4.21116  2.71668  3.64495  4.43195  4.66188  4.35829  3.99238  3.10363  2.02207  1.89528  5.14692  3.02155      2 f - - -
            2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
            0.00661  5.41881  6.14115  0.61958  0.77255  0.61842  0.77391
  
  
original_text: 2026: <p>I am trying to recreate the experiment from <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5348765/" rel="noreferrer"><em>Convergence of retrotransposons in
  oomycetes and plants</em></a> by Kirill Ustyantsev, Alexandr Blinov and Georgy Smyshlyaev. In the "Methods" section a </p>
  
  <blockquote>
    <p>HMM profile was constructed from the amino acid alignment of aRNH
    sequences from the Ustyantsev et al</p>
  </blockquote>
  
  <p>I was wondering where I could get this profile. I checked the cited papers but they were also referencing other papers. Could someone maybe clarify where I could get the profile?</p>
   298: <p>The alignment they used to build the HMM is included as <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5348765/bin/13100_2017_87_MOESM8_ESM.txt" rel="nofollow noreferrer">supplementary file 8</a> in the paper you cite:</p>
  
  <blockquote>
    <p>Multiple amino acid sequence alignment of RNH genes and domains from diverse taxa constructed and used for the phylogenetic reconstruction in the present study. (TXT 45 kb)</p>
  </blockquote>
  
  <p>So, you can download that alignment and then use a tool like hmmbuild (part of <a href="http://hmmer.org/" rel="nofollow noreferrer">HMMER</a>) to build the HMM profile:</p>
  
  <pre><code>hmmbuild model.hmm 13100_2017_87_MOESM8_ESM.txt 
  </code></pre>
  
  <p>The command above will create the file <code>model.hmm</code> which contains the HMM built from the alignment in the supplementary file <code>13100_2017_87_MOESM8_ESM.txt</code>. I am including the first few lines here (this is <em>not</em> the entire file, don't use this as the model—build it yourself. I only include it to illustrate the format): </p>
  
  <pre><code>HMMER3/f [3.1b2 | February 2015]
  NAME  13100_2017_87_MOESM8_ESM
  LENG  121
  ALPH  amino
  RF    no
  MM    no
  CONS  yes
  CS    no
  MAP   yes
  DATE  Mon Dec 11 13:33:29 2017
  NSEQ  165
  EFFN  5.697556
  CKSUM 2893352190
  STATS LOCAL MSV       -9.8975  0.71332
  STATS LOCAL VITERBI  -10.6450  0.71332
  STATS LOCAL FORWARD   -3.9247  0.71332
  HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y   
              m-&gt;m     m-&gt;i     m-&gt;d     i-&gt;m     i-&gt;i     d-&gt;m     d-&gt;d
    COMPO   2.34473  4.21240  2.85435  2.69203  3.54228  2.79153  3.54812  3.01140  2.72630  2.48370  3.82225  2.94269  3.49156  3.05882  2.84632  2.63343  2.86306  2.72633  4.27012  3.56181
            2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
            0.13773  5.45955  2.08419  0.61958  0.77255  0.00000        *
        1   2.99488  4.57852  4.44659  3.29307  1.80597  4.16203  3.88788  2.87265  3.75733  2.38594  3.30344  3.33633  4.53284  3.64324  3.69630  2.90350  3.30742  2.83413  4.36991  1.50673      1 y - - -
            2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
            0.00723  5.32905  6.05140  0.61958  0.77255  0.45275  1.01027
        2   2.66602  2.17750  5.01715  4.40788  1.72617  4.29647  4.62737  2.89579  4.21116  2.71668  3.64495  4.43195  4.66188  4.35829  3.99238  3.10363  2.02207  1.89528  5.14692  3.02155      2 f - - -
            2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
            0.00661  5.41881  6.14115  0.61958  0.77255  0.61842  0.77391
  </code></pre>
  