Answers.Body: <p>In my personal experience, MUSCLE is the easiest program to use in conjunction with Biopython. Biopython features a <a href="https://biopython.org/docs/1.75/api/Bio.Align.Applications.html" rel="nofollow noreferrer">command line wrapper</a> for this program, which makes it very easy to use. Make sure to <a href="http://www.drive5.com/muscle/downloads.htm" rel="nofollow noreferrer">download the appropriate MUSCLE program from drive5</a> and save it somewhere. E.g., if you are using Jupyter in Linux:</p>
  <pre><code>!wget https://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
  !tar -xzvf muscle3.8.31_i86linux64.tar.gz
  !cp muscle3.8.31_i86linux64 /usr/local/bin
  !chmod 755 /usr/local/bin/muscle3.8.31_i86linux64
  </code></pre>
  <p>Then, you can run MUSCLE like so:</p>
  <pre><code>from Bio.Align.Applications import MuscleCommandline
  def runMUSCLE(infile, outfile):
      muscle_exe = r&quot;/usr/local/bin/muscle3.8.31_i86linux64&quot; #Here is where we installed MUSCLE
      muscle_cline = MuscleCommandline(muscle_exe,
                                       input=infile,
                                       out=outfile,
                                       clwstrict=True #Output in clustal format (more visually pleasing), otherwise the output is in FASTA. Whichever you need.
                                      )
      muscle_cline()
  </code></pre>
  <p>You don't need to specify that your sequence is amino acidic, however keep in mind that the input file must be in FASTA format.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-01-08T11:30:22.840Z
Answers.LastActivityDate: 2021-01-08T11:30:22.840Z
Answers.UserDisplayName: albertr
Body: <p>I am very new to bioinformatics (and python in general), but I would like to use python to more efficiently analyse enzymes both in terms of structure and functio, using Jupiter notebook. I would like to ask what is the best program/source code for multiple sequence alignments (amino acids) to identify conserved binding sites etc. I see that <a href="https://biopython.org/docs/1.74/api/index.html#" rel="nofollow noreferrer">biopython</a> has a few ways of creating alignments, but I have the impression that it is more focused on nucleotide sequences?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-02T08:18:53.530Z
Comments.Text: It works for both —but for global alignments you'd want system calls to something better (`muscle` say) than the inbuilt pairwise method. I don't know about MSA viewers for Jupyter, but I'd like to say that `nglview` is a really nice module to view your 3D protein structure in the notebook —it is despotic to set up at times, but totally worth the struggle.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-03T09:50:23.580Z
Comments.Text: Thanks, yea I got nglview to work after some time! Still working on the MSA in python, most sites seem to focus on nucleotide alignments.
Comments.UserDisplayName: CuriousTree
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-26T14:21:42.947Z
Comments.Text: I found [a nice blog post](https://dmnfarrell.github.io/bioinformatics/bokeh-sequence-aligner) about plotting MSAs in Jupyter notebooks, which I thought was relevant to this.
Comments.UserDisplayName: Matteo Ferla
Tags: <phylogenetics><proteins><python>
Title: MSA (protein) with biopython or something else?
ThreadText: # MSA (protein) with biopython or something else?
  
  (Asked by: username_0 on 2020-05-01)
  
  I am very new to bioinformatics (and python in general), but I would like to use python to more efficiently analyse enzymes both in terms of structure and functio, using Jupiter notebook. I would like to ask what is the best program/source code for multiple sequence alignments (amino acids) to identify conserved binding sites etc. I see that [biopython](https://biopython.org/docs/1.74/api/index.html#) has a few ways of creating alignments, but I have the impression that it is more focused on nucleotide sequences?
  
  **Tags:** phylogenetics, proteins, python
  
  > **Comments:**
  > **username_1**: It works for both —but for global alignments you'd want system calls to something better (`muscle` say) than the inbuilt pairwise method. I don't know about MSA viewers for Jupyter, but I'd like to say that `nglview` is a really nice module to view your 3D protein structure in the notebook —it is despotic to set up at times, but totally worth the struggle.  
  > **username_0**: Thanks, yea I got nglview to work after some time! Still working on the MSA in python, most sites seem to focus on nucleotide alignments.  
  > **username_1**: I found [a nice blog post](https://dmnfarrell.github.io/bioinformatics/bokeh-sequence-aligner) about plotting MSAs in Jupyter notebooks, which I thought was relevant to this.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2021-01-08. Score: 1
  
  In my personal experience, MUSCLE is the easiest program to use in conjunction with Biopython. Biopython features a [command line wrapper](https://biopython.org/docs/1.75/api/Bio.Align.Applications.html) for this program, which makes it very easy to use. Make sure to [download the appropriate MUSCLE program from drive5](http://www.drive5.com/muscle/downloads.htm) and save it somewhere. E.g., if you are using Jupyter in Linux:
  
  ```
  !wget https://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
  !tar -xzvf muscle3.8.31_i86linux64.tar.gz
  !cp muscle3.8.31_i86linux64 /usr/local/bin
  !chmod 755 /usr/local/bin/muscle3.8.31_i86linux64
  
  ```
  
  Then, you can run MUSCLE like so:
  
  ```
  from Bio.Align.Applications import MuscleCommandline
  def runMUSCLE(infile, outfile):
      muscle_exe = r"/usr/local/bin/muscle3.8.31_i86linux64" #Here is where we installed MUSCLE
      muscle_cline = MuscleCommandline(muscle_exe,
                                       input=infile,
                                       out=outfile,
                                       clwstrict=True #Output in clustal format (more visually pleasing), otherwise the output is in FASTA. Whichever you need.
                                      )
      muscle_cline()
  
  ```
  
  You don't need to specify that your sequence is amino acidic, however keep in mind that the input file must be in FASTA format.
  
  
  ---
  
  