Answers.Body: <p>The general procedure is:</p>
  
  <ol>
  <li>Find the sequence for the same (or as similar as you can find (see mentions of blast in the comments above)) gene in other species. You can use uniprot or any other large sequence database for this.</li>
  <li>You now have a large set of sequences related to yours, which you'll need to compare. Search the methods section of your favorite paper to see how they reconstructed likely evolutionary history from this, there are a number of packages out there.</li>
  </ol>
  
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Answers.CreationDate: 2018-01-25T13:47:27.583Z
Answers.Text: My main concern is why these construction methods are plausible.
Answers.UserDisplayName: 0x90
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Answers.Text: The exact same way we can infer what proto-indo-european words for things were...
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-25T13:52:57.347Z
Answers.Text: lol how do linguists do this indeed? Also for languages you have ancient texts.
Answers.UserDisplayName: 0x90
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Answers.UserDisplayName: Devon Ryan
Answers.Body: <p><a href="https://i.sstatic.net/cDkJT.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/cDkJT.jpg" alt="enter image description here"></a></p>
  
  <p>There you go, its Microcystis aeruginosa aspartate/glutamate racemase. Easy does it. If you want to know how you can do this in 15 seconds let me know.</p>
  
  <hr>
  
  <p>Its one of the new features of NCBI's Blast</p>
  
  <ol>
  <li>Go to Blast here, <a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi" rel="nofollow noreferrer">https://blast.ncbi.nlm.nih.gov/Blast.cgi</a></li>
  <li>Enter your sequence into the box (it doesn't accept PDB codes alone)</li>
  <li>Enter the protein database - when I first did this calculation I used SwissProt, thinking there would be alot of sequences - I then used "nr"</li>
  <li>Under the algorithm parameters enter "50" (default is too many)</li>
  <li>Hit "Blast"</li>
  <li>Once the search is complete at the top of the page are the hyperlinks:
  "Other reports: Search Summary [Taxonomy reports] [Distance tree of results]"</li>
  <li>Click on "Distance tree of results"</li>
  <li>The following page will load automatically, automatically aligning your sequences and producing, in this case a parsimony based tree, but there is also the option of a nj tree (recommended) .... here: <a href="https://www.ncbi.nlm.nih.gov/blast/treeview/treeView.cgi?request=page&amp;blastRID=5A1ZBRU1014&amp;queryID=lcl%7CQuery_210080&amp;entrezLim=&amp;ex=&amp;exl=&amp;exh=&amp;ns=50&amp;screenWidth=1280&amp;screenHeight=800" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/blast/treeview/treeView.cgi?request=page&amp;blastRID=5A1ZBRU1014&amp;queryID=lcl|Query_210080&amp;entrezLim=&amp;ex=&amp;exl=&amp;exh=&amp;ns=50&amp;screenWidth=1280&amp;screenHeight=800</a></li>
  <li>Click "Tool", "Download", "PDF" ...</li>
  </ol>
  
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Answers.CreationDate: 2019-02-02T03:06:29.507Z
Answers.LastActivityDate: 2019-02-03T18:54:45.577Z
Answers.LastEditDate: 2019-02-03T18:54:45.577Z
Answers.UserDisplayName: M__
Body: <p>I'd like to build the <a href="https://embnet.vital-it.ch/CoursEMBnet/PHYL03/Slides/Protein_II_Phylogeny_2.pdf" rel="nofollow noreferrer">evolutionary history of a protein</a>, given its sequence. Namely, given a FASTA entry how can I build an evolutionary tree? Here is the <a href="https://www.rcsb.org/structure/5WXY" rel="nofollow noreferrer">5wxy</a> protein as an example:</p>
  <pre><code>&gt;5WXY:A|PDBID|CHAIN|SEQUENCE
  MGHHHHHHMMKTKLPILGVLGGMGPVVTAEFLKSIYEYNPFIDKEQESPNVIVFSFPSAPDRTGSIDSGKEREFIDFIQV
  NLEHLNKLADCIVIGSCTAHYALPQIPENLKDKLISLIKIADQELQEYNEPTLLLASTGTYQKKLFQEGCTTADLIISLS
  ESDQKLIHEMIYKVLKRGHDPLSILRDIEALLEKYNTRSYISGSTEFHLLTKSLKLKGIDSIKAIDPLSTIAQNFSQLII
  KQAQVDLVTDCHQPSNPKSP
  </code></pre>
  <p>Do I need to do some queries to <a href="https://bioinformatics.stackexchange.com/questions/2128/getting-protein-fasta-sequence-based-on-keyword-with-python">Entrez</a> in order to build the evolution tree?</p>
  <p>I saw <a href="http://nature.com/articles/srep06504" rel="nofollow noreferrer">this</a> paper, but I am not sure how I can use it with a single mammal's protein primary sequence.</p>
  <hr />
  <p><strong>Question</strong> given a protein name, is it possible to look for its evolutionary history or build evolution tree using other databases beside <a href="https://www.rcsb.org/search" rel="nofollow noreferrer">PDB</a> on top of bioinformatics algorithms.</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-24T15:08:48.280Z
Comments.Text: You can’t build an evolutionary tree given a single data point (e.g. a single protein sequence). A tree *relates multiple data points*. Could you therefore please clarify what your input and desired output are?
Comments.UserDisplayName: Konrad Rudolph
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-24T15:12:12.303Z
Comments.Text: @KonradRudolph, I would like to a protein from the PDB and find/generate its evolutionary tree.
Comments.UserDisplayName: 0x90
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-24T15:16:43.727Z
Comments.Text: Now you’ve just restated the question. But as I tried to explain, this doesn’t make sense.
Comments.UserDisplayName: Konrad Rudolph
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-24T15:19:19.233Z
Comments.Text: @KonradRudolph I see what you are saying. Though how comes other people create such trees? for example (this paper) [http://www.pnas.org/content/108/20/8329.full].
Comments.UserDisplayName: 0x90
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-24T18:29:08.310Z
Comments.Text: The trees in that paper relate many different *E. coli* strains, which is exactly my point: rather than having a single data point, they are comparing several different ones.
Comments.UserDisplayName: Konrad Rudolph
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-24T18:30:33.127Z
Comments.Text: @KonradRudolph so is there a database that associates a protein to its family etc.? I am not saying it's possible to get the whole tree from a single node. Of course it's not possible. My question is how can I do it using other resources given a PDB name.
Comments.UserDisplayName: 0x90
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-25T08:08:51.233Z
Comments.Text: Given a PDB identifier and sequence, one can use other databases like NCBI nucleotide database to find other related sequences (using psi-blast) to build a tree. All the resources you linked had a multiple comparison/alignment in its workflow, so you need other resources aside from PDB
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-25T12:14:33.723Z
Comments.Text: @Llopis is there DB for amino acids database? Or an example for how to use what you have suggested? (Using NCBI/psi-blast)
Comments.UserDisplayName: 0x90
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-25T12:28:04.410Z
Comments.Text: There's [uniprot](http://www.uniprot.org/), and you can use blast from protein to DNA. That is far away from your question. I'm just trying to help you to redirect your question for you to get answer. What have you tried/searched? I can spend some time helping people but if people don't spend time helping themselves I won't.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-25T12:39:29.697Z
Comments.Text: @Llopis what's blast? At the moment I try to understand what I need to know in order to find the evolutionary tree for a PDB entry.
Comments.UserDisplayName: 0x90
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-25T12:40:52.680Z
Comments.Text: Did you seach for it ? "blast bioinformatics" will lead you on the path
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-25T13:31:55.103Z
Comments.Text: @Llopis, yes I ran it. What did you have in mind to do with it and http://www.uniprot.org? 
  The results: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=6KNTUB6D016
Comments.UserDisplayName: 0x90
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-25T13:34:19.083Z
Comments.Text: @0x90 What do you think was meant? You need to put a modicum of effort into things.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-25T13:37:27.493Z
Comments.Text: @DevonRyan I am asking for a general direction of what to do uniport offers various number of tools and I am not sure what should I do. I want to understand the idea of how to do it first rather to run bunch of tools without understanding.
Comments.UserDisplayName: 0x90
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-25T13:40:01.100Z
Comments.Text: @DevonRyan one of my problems is why it would be even possible to do evolution in reverse. I would expect evolution to be a irreversible process.
Comments.UserDisplayName: 0x90
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-25T14:09:23.390Z
Comments.Text: @0x90 If you are not sure what to do search for it, if even so you can't then solve your problem, then ask, but not the other way round, please. If you need more training you can take courses, there are some online courses very interesting
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-25T14:37:28.867Z
Comments.Text: @Llopis I think what you guys gave me so far should give me some general idea to start with. If you have good idea for a course/reference on evolution in bioinformatics please let me know.
Comments.UserDisplayName: 0x90
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-25T14:54:48.797Z
Comments.Text: I am not informed of the online courses, but I'm sure you will find some, you can check back for opinions in the [chat] (if you want some).
Comments.UserDisplayName: llrs
Tags: <phylogenetics><proteins><phylogeny><pdb>
Title: How to find/build the evolutionary history of a protein from its sequence?
ThreadText: # How to find/build the evolutionary history of a protein from its sequence?
  
  (Asked by: username_0 on 2018-01-23)
  
  I'd like to build the [evolutionary history of a protein](https://embnet.vital-it.ch/CoursEMBnet/PHYL03/Slides/Protein_II_Phylogeny_2.pdf), given its sequence. Namely, given a FASTA entry how can I build an evolutionary tree? Here is the [5wxy](https://www.rcsb.org/structure/5WXY) protein as an example:
  
  ```
  >5WXY:A|PDBID|CHAIN|SEQUENCE
  MGHHHHHHMMKTKLPILGVLGGMGPVVTAEFLKSIYEYNPFIDKEQESPNVIVFSFPSAPDRTGSIDSGKEREFIDFIQV
  NLEHLNKLADCIVIGSCTAHYALPQIPENLKDKLISLIKIADQELQEYNEPTLLLASTGTYQKKLFQEGCTTADLIISLS
  ESDQKLIHEMIYKVLKRGHDPLSILRDIEALLEKYNTRSYISGSTEFHLLTKSLKLKGIDSIKAIDPLSTIAQNFSQLII
  KQAQVDLVTDCHQPSNPKSP
  
  ```
  
  Do I need to do some queries to [Entrez](https://bioinformatics.stackexchange.com/questions/2128/getting-protein-fasta-sequence-based-on-keyword-with-python) in order to build the evolution tree?
  
  I saw [this](http://nature.com/articles/srep06504) paper, but I am not sure how I can use it with a single mammal's protein primary sequence.
  
  ---
  
  **Question** given a protein name, is it possible to look for its evolutionary history or build evolution tree using other databases beside [PDB](https://www.rcsb.org/search) on top of bioinformatics algorithms.
  
  **Tags:** phylogenetics, proteins, phylogeny, pdb
  
  > **Comments:**
  > **username_1**: You can’t build an evolutionary tree given a single data point (e.g. a single protein sequence). A tree *relates multiple data points*. Could you therefore please clarify what your input and desired output are?  
  > **username_0**: @username_1, I would like to a protein from the PDB and find/generate its evolutionary tree.  
  > **username_1**: Now you’ve just restated the question. But as I tried to explain, this doesn’t make sense.  
  > **username_0**: @username_1 I see what you are saying. Though how comes other people create such trees? for example (this paper) [http://www.pnas.org/content/108/20/8329.full].  
  > **username_1**: The trees in that paper relate many different *E. coli* strains, which is exactly my point: rather than having a single data point, they are comparing several different ones.  
  > **username_0**: @username_1 so is there a database that associates a protein to its family etc.? I am not saying it's possible to get the whole tree from a single node. Of course it's not possible. My question is how can I do it using other resources given a PDB name.  
  > **username_2**: Given a PDB identifier and sequence, one can use other databases like NCBI nucleotide database to find other related sequences (using psi-blast) to build a tree. All the resources you linked had a multiple comparison/alignment in its workflow, so you need other resources aside from PDB  
  > **username_0**: @Llopis is there DB for amino acids database? Or an example for how to use what you have suggested? (Using NCBI/psi-blast)  
  > **username_2**: There's [uniprot](http://www.uniprot.org/), and you can use blast from protein to DNA. That is far away from your question. I'm just trying to help you to redirect your question for you to get answer. What have you tried/searched? I can spend some time helping people but if people don't spend time helping themselves I won't.  
  > **username_0**: @Llopis what's blast? At the moment I try to understand what I need to know in order to find the evolutionary tree for a PDB entry.  
  > **username_2**: Did you seach for it ? "blast bioinformatics" will lead you on the path  
  > **username_0**: @Llopis, yes I ran it. What did you have in mind to do with it and http://www.uniprot.org?  The results: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=6KNTUB6D016  
  > **username_3**: @username_0 What do you think was meant? You need to put a modicum of effort into things.  
  > **username_0**: @username_3 I am asking for a general direction of what to do uniport offers various number of tools and I am not sure what should I do. I want to understand the idea of how to do it first rather to run bunch of tools without understanding.  
  > **username_0**: @username_3 one of my problems is why it would be even possible to do evolution in reverse. I would expect evolution to be a irreversible process.  
  > **username_2**: @username_0 If you are not sure what to do search for it, if even so you can't then solve your problem, then ask, but not the other way round, please. If you need more training you can take courses, there are some online courses very interesting  
  > **username_0**: @Llopis I think what you guys gave me so far should give me some general idea to start with. If you have good idea for a course/reference on evolution in bioinformatics please let me know.  
  > **username_2**: I am not informed of the online courses, but I'm sure you will find some, you can check back for opinions in the [chat] (if you want some).  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2018-01-25. Score: 3
  
  The general procedure is:
  
  1. Find the sequence for the same (or as similar as you can find (see mentions of blast in the comments above)) gene in other species. You can use uniprot or any other large sequence database for this.
  2. You now have a large set of sequences related to yours, which you'll need to compare. Search the methods section of your favorite paper to see how they reconstructed likely evolutionary history from this, there are a number of packages out there.
  
  > **Comments:**
  > **username_0**: My main concern is why these construction methods are plausible.  
  > **username_3**: The exact same way we can infer what proto-indo-european words for things were...  
  > **username_0**: lol how do linguists do this indeed? Also for languages you have ancient texts.  
  
  ---
  
  ### Answer by username_4 on 2019-02-02. Score: 2
  
  [![enter image description here](https://i.sstatic.net/cDkJT.jpg)](https://i.sstatic.net/cDkJT.jpg)
  
  There you go, its Microcystis aeruginosa aspartate/glutamate racemase. Easy does it. If you want to know how you can do this in 15 seconds let me know.
  
  ---
  
  Its one of the new features of NCBI's Blast
  
  1. Go to Blast here, <https://blast.ncbi.nlm.nih.gov/Blast.cgi>
  2. Enter your sequence into the box (it doesn't accept PDB codes alone)
  3. Enter the protein database - when I first did this calculation I used SwissProt, thinking there would be alot of sequences - I then used "nr"
  4. Under the algorithm parameters enter "50" (default is too many)
  5. Hit "Blast"
  6. Once the search is complete at the top of the page are the hyperlinks:
     "Other reports: Search Summary [Taxonomy reports] [Distance tree of results]"
  7. Click on "Distance tree of results"
  8. The following page will load automatically, automatically aligning your sequences and producing, in this case a parsimony based tree, but there is also the option of a nj tree (recommended) .... here: [https://www.ncbi.nlm.nih.gov/blast/treeview/treeView.cgi?request=page&blastRID=5A1ZBRU1014&queryID=lcl|Query\_210080&entrezLim=&ex=&exl=&exh=&ns=50&screenWidth=1280&screenHeight=800](https://www.ncbi.nlm.nih.gov/blast/treeview/treeView.cgi?request=page&blastRID=5A1ZBRU1014&queryID=lcl%7CQuery_210080&entrezLim=&ex=&exl=&exh=&ns=50&screenWidth=1280&screenHeight=800)
  9. Click "Tool", "Download", "PDF" ...
  
  
  ---
  
  