<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>

CC BY-SA 3.0
2017-12-11T11:48:29.407Z
thanks for the clarification. I missed the additional file since I was looking at a printed out copy.
A.Dumas
CC BY-SA 3.0
2017-12-11T11:36:49.780Z
2017-12-11T11:36:49.780Z
terdon
<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>

CC BY-SA 3.0
2017-12-11T11:22:08.423Z
Your question is how to to this HMM or how to obtain/download it? In the later case you can always try to contact the authors if it is important to use exactly the same HMM profile
llrs
<hidden-markov-models>
HMM Profile from Convergence of retrotransposons in oomycetes and plants
# HMM Profile from Convergence of retrotransposons in oomycetes and plants

(Asked by: username_0 on 2017-12-11)

I am trying to recreate the experiment from [*Convergence of retrotransposons in
oomycetes and plants*](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5348765/) 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?

**Tags:** hidden-markov-models
> **Comments:**
> **username_1**: Your question is how to to this HMM or how to obtain/download it? In the later case you can always try to contact the authors if it is important to use exactly the same HMM profile  

---

## 1 answers

### Answer by username_2 on 2017-12-11. Score: 2 | Accepted answer

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

> **Comments:**
> **username_0**: thanks for the clarification. I missed the additional file since I was looking at a printed out copy.  

---

