Answers.Body: <h2>Q - Is there some parameter for this?</h2>
  
  <p>No, there is no parameter for this. Getting the conserved regions is something that you will have to perform post-alignment. </p>
  
  <h2>How to get the conserved regions?</h2>
  
  <p>You will need to define what exactly you mean by conservation and calculate a conservation score for each position of the alignment.</p>
  
  <p>For instance you can look at each column of the alignment and calculate the percent of queries that had the same base/AA at that position. If using AAs you can define conservation more loosely depending on what properties are important to you, or using a scoring matrix.</p>
  
  <p>Once you have a co-occurrence matrix you can define the regions of interest based on a conservation threshold that you define.</p>
  
  <h2>Is there software to find conserved columns?</h2>
  
  <p>There is a program <a href="https://github.com/gcollet/MstatX" rel="nofollow noreferrer">MstatX</a> which outputs conservation scores of individual columns.</p>
  
  <h2>How MstatX works</h2>
  
  <p>The example of MstatX provides this example alignment. Each column is progressively less conserved than the last. The last column is conserved, but has some gaps -- this lowers the conservation score.</p>
  
  <pre><code>   col          1
   seq1  1234567890
   seq2  DDDDDDIPDL
   seq3  DDDDDDIPVL
   seq4  DDDDDDIPYL
   seq5  DDDDDDIPA-
   seq6  DDDDDDLWT-
   seq7  DDEDEELWK-
   seq8  DDEDEELWP-
   seq9  DDEDEFVSR-
   seq10 DEEFFFVSH-
  </code></pre>
  
  <p>The conservation scores for each column were:</p>
  
  <pre><code>1       2.71272e-08
  2       0.243433
  3       0.312789
  4       0.243433
  5       0.483364
  6       0.480391
  7       0.498757
  8       0.498757
  9       0.973514
  10      0.267319
  </code></pre>
  
  <h2>How to get conserved regions</h2>
  
  <p>The python program below will output all windows of conserved regions when using a fasta alignment and the default output from <code>MstatX</code>.</p>
  
  <ul>
  <li>Positional args 
  
  <ul>
  <li><strong>1.</strong> <code>MstatX_alignment_example.mali</code>, is the fasta alignment file. </li>
  <li><strong>2.</strong> <code>output.txt</code> is the default output of <code>mstatx</code> when called with <code>mstatx -i MstatX_alignment_example.mali</code>. </li>
  <li><strong>3.</strong> 0.4 is the minimum conservation score</li>
  <li><strong>4.</strong> 3 is the minimum number of bases that must have that conservation score.</li>
  </ul></li>
  </ul>
  
  <p>Calling this program with the following command on the above example: </p>
  
  <p><code>python print_conserved_regions.py MstatX_alignment_example.mali output.txt 0.4 3</code> prints:</p>
  
  <pre><code>{1,4}
  </code></pre>
  
  <p>Meaning that there was only one window at least 3 bases long in which all positions had a conservation score below 0.4. This window was positions 1 through 4 in the alignment.</p>
  
  <pre class="lang-py prettyprint-override"><code>#call this file cons_windows.py
  import sys
  from Bio import AlignIO
  
  align_filename = sys.argv[1]
  cons_filename = sys.argv[2]
  cutoff = float(sys.argv[3])
  minchar = int(sys.argv[4])
  
  def parse_conservation(filename):
      cons = {}
      with open(filename, "r") as f:
          for line in f:
              if line.strip():
                  temp = line.split()
                  cons[int(temp[0])] = float(temp[1])
      return cons
  
  align = AlignIO.read(align_filename, "fasta")
  cons = parse_conservation(sys.argv[2])
  
  i = 1
  while i &lt; max(cons):
      if cons[i] &lt;= cutoff:
          j = i
          done = False
          while j &lt; max(cons) and not done:
              if (cons[j] &gt; cutoff) and (j-i &gt;= minchar):
                  print("{{{},{}}}".format(i,j-1))
                  done = True
                  i = j
              j+=1
      i+=1
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-01-30T20:19:03.780Z
Answers.LastActivityDate: 2019-01-30T20:56:06.883Z
Answers.LastEditDate: 2019-01-30T20:56:06.883Z
Answers.UserDisplayName: conchoecia
Body: <p>So I aligned roughly 5k sequences and I got my output using mafft. However, I want to restrict the output to only present conserved segments of a specific length (let's say 25bp). Does mafft have parameters to set this that I seem to be missing?</p>
  
Tags: <phylogenetics>
Title: Restricting match output for multiple sequence alignment using mafft?
ThreadText: # Restricting match output for multiple sequence alignment using mafft?
  
  (Asked by: username_0 on 2019-01-30)
  
  So I aligned roughly 5k sequences and I got my output using mafft. However, I want to restrict the output to only present conserved segments of a specific length (let's say 25bp). Does mafft have parameters to set this that I seem to be missing?
  
  **Tags:** phylogenetics
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-01-30. Score: 2
  
  ## Q - Is there some parameter for this?
  
  No, there is no parameter for this. Getting the conserved regions is something that you will have to perform post-alignment.
  
  ## How to get the conserved regions?
  
  You will need to define what exactly you mean by conservation and calculate a conservation score for each position of the alignment.
  
  For instance you can look at each column of the alignment and calculate the percent of queries that had the same base/AA at that position. If using AAs you can define conservation more loosely depending on what properties are important to you, or using a scoring matrix.
  
  Once you have a co-occurrence matrix you can define the regions of interest based on a conservation threshold that you define.
  
  ## Is there software to find conserved columns?
  
  There is a program [MstatX](https://github.com/gcollet/MstatX) which outputs conservation scores of individual columns.
  
  ## How MstatX works
  
  The example of MstatX provides this example alignment. Each column is progressively less conserved than the last. The last column is conserved, but has some gaps -- this lowers the conservation score.
  
  ```
     col          1
   seq1  1234567890
   seq2  DDDDDDIPDL
   seq3  DDDDDDIPVL
   seq4  DDDDDDIPYL
   seq5  DDDDDDIPA-
   seq6  DDDDDDLWT-
   seq7  DDEDEELWK-
   seq8  DDEDEELWP-
   seq9  DDEDEFVSR-
   seq10 DEEFFFVSH-
  
  ```
  
  The conservation scores for each column were:
  
  ```
  1       2.71272e-08
  2       0.243433
  3       0.312789
  4       0.243433
  5       0.483364
  6       0.480391
  7       0.498757
  8       0.498757
  9       0.973514
  10      0.267319
  
  ```
  
  ## How to get conserved regions
  
  The python program below will output all windows of conserved regions when using a fasta alignment and the default output from `MstatX`.
  
  * Positional args
    + **1.** `MstatX_alignment_example.mali`, is the fasta alignment file.
    + **2.** `output.txt` is the default output of `mstatx` when called with `mstatx -i MstatX_alignment_example.mali`.
    + **3.** 0.4 is the minimum conservation score
    + **4.** 3 is the minimum number of bases that must have that conservation score.
  
  Calling this program with the following command on the above example:
  
  `python print_conserved_regions.py MstatX_alignment_example.mali output.txt 0.4 3` prints:
  
  ```
  {1,4}
  
  ```
  
  Meaning that there was only one window at least 3 bases long in which all positions had a conservation score below 0.4. This window was positions 1 through 4 in the alignment.
  
  ```py
  #call this file cons_windows.py
  import sys
  from Bio import AlignIO
  
  align_filename = sys.argv[1]
  cons_filename = sys.argv[2]
  cutoff = float(sys.argv[3])
  minchar = int(sys.argv[4])
  
  def parse_conservation(filename):
      cons = {}
      with open(filename, "r") as f:
          for line in f:
              if line.strip():
                  temp = line.split()
                  cons[int(temp[0])] = float(temp[1])
      return cons
  
  align = AlignIO.read(align_filename, "fasta")
  cons = parse_conservation(sys.argv[2])
  
  i = 1
  while i < max(cons):
      if cons[i] <= cutoff:
          j = i
          done = False
          while j < max(cons) and not done:
              if (cons[j] > cutoff) and (j-i >= minchar):
                  print("{{{},{}}}".format(i,j-1))
                  done = True
                  i = j
              j+=1
      i+=1
  
  ```
  
  
  ---
  
  