Body: <p>I’d like to perform the following, but I am having difficulty.</p>
  <p>I want to convert amino acid sequences in multifasta files into matrices (or vectors) with Euclidean distance and Pearson correlation coefficient.</p>
  <p>If you know a solution, please let me know. Thanking you in advance.</p>
  <h3>File1</h3>
  <pre><code>&gt;BDP27474.1 |surface glycoprotein [Severe acute respiratory syndrome coronavirus 2]
  MFVFLVLLPL
  &gt;BDP27485.1 |surface glycoprotein [Severe acute respiratory syndrome coronavirus 2]
  MFVFLVLLPL
  </code></pre>
  <h3>File2</h3>
  <pre><code>&gt;BDD77411.1 |surface glycoprotein [Severe acute respiratory syndrome coronavirus 2]
  MFVFLVLLPL
  &gt;BDD77515.1 |surface glycoprotein [Severe acute respiratory syndrome coronavirus 2]
  MFVFFVLLPL
  </code></pre>
  <h3>Code</h3>
  <pre><code>library(tidyverse)
  library(ape)
  library(Biostrings)
  
  naseq1 &lt;- readAAStringSet(&quot;File1.fasta&quot;)
  naseq2 &lt;- readAAStringSet(&quot;File2.fasta&quot;)
  
  dist.aa(naseq1)
  dist.aa(naseq2)
  
  ##Error in numeric(n * (n - 1)/2) : invalid 'length' argument
  </code></pre>
  <h3>Add info.</h3>
  <p>iOS 10.15, Rstudio cloud</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-07-26T15:19:27.083Z
Comments.Text: There's no matrix for file1 because MFVFLVLLPL and MFVFLVLLPL are identical
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-07-27T08:13:10.030Z
Comments.Text: You are probably looking for Biostrings::stringDist to compare both strings
Comments.UserDisplayName: llrs
Tags: <fasta><r>
Title: How to calculate distance matrix from fasta?
ThreadText: # How to calculate distance matrix from fasta?
  
  (Asked by: username_0 on 2022-07-25)
  
  I’d like to perform the following, but I am having difficulty.
  
  I want to convert amino acid sequences in multifasta files into matrices (or vectors) with Euclidean distance and Pearson correlation coefficient.
  
  If you know a solution, please let me know. Thanking you in advance.
  
  ### File1
  
  ```
  >BDP27474.1 |surface glycoprotein [Severe acute respiratory syndrome coronavirus 2]
  MFVFLVLLPL
  >BDP27485.1 |surface glycoprotein [Severe acute respiratory syndrome coronavirus 2]
  MFVFLVLLPL
  
  ```
  
  ### File2
  
  ```
  >BDD77411.1 |surface glycoprotein [Severe acute respiratory syndrome coronavirus 2]
  MFVFLVLLPL
  >BDD77515.1 |surface glycoprotein [Severe acute respiratory syndrome coronavirus 2]
  MFVFFVLLPL
  
  ```
  
  ### Code
  
  ```
  library(tidyverse)
  library(ape)
  library(Biostrings)
  
  naseq1 <- readAAStringSet("File1.fasta")
  naseq2 <- readAAStringSet("File2.fasta")
  
  dist.aa(naseq1)
  dist.aa(naseq2)
  
  ##Error in numeric(n * (n - 1)/2) : invalid 'length' argument
  
  ```
  
  ### Add info.
  
  iOS 10.15, Rstudio cloud
  
  **Tags:** fasta, r
  
  > **Comments:**
  > **username_1**: There's no matrix for file1 because MFVFLVLLPL and MFVFLVLLPL are identical  
  > **username_2**: You are probably looking for Biostrings::stringDist to compare both strings  
  
  ---
  
  ## 0 answers
  
  