Answers.Body: <p>Click on the 'GenBank' dropdown menu at the top left corner of <a href="https://www.ncbi.nlm.nih.gov/nuccore/BA000005.3" rel="nofollow noreferrer">this page</a> to see a <a href="https://www.ncbi.nlm.nih.gov/nuccore/BA000005.3?report=graph" rel="nofollow noreferrer">graphical view</a> of the sequence. You should see a 'Repeat region' track in the Sequence Viewer. Click on the 'Download' button in the top right corner of the Sequence Viewer, choose 'Download Track Data' to launch a dialog box where you can enter a range, select the 'Repeat region' track and download data in BED format. Unfortunately, the names for the features are not great.</p>
  <p>If you want the names to be the same ones in the flat file, you can download the feature table and parse it. To download the feature table, click on the 'Send To' link at the top right corner of <a href="https://www.ncbi.nlm.nih.gov/nuccore/BA000005.3" rel="nofollow noreferrer">this page</a>, choose 'Complete Record', 'File' and 'Feature Table' as 'Format'. After you download the feature table, you can parse it using <code>awk</code> as shown below to create a 4-column table with the data.</p>
  <pre><code>cat seq.ft \
    | awk 'BEGIN{FS=&quot;\t&quot;;OFS=&quot;\t&quot;}{
      if(NF==3) {print s,e,f,q ; s=$1; e=$2; f=$3; q=&quot;&quot;} 
      else if(NF==2) {print s,e,f,q ; s=$1; e=$2; q=&quot;&quot;} 
      else if(NF==5) {q=q&quot;|&quot;$4&quot;=&quot;$5} }' \
    &gt; feat_table.tsv
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-11T01:30:17.137Z
Answers.LastActivityDate: 2020-07-11T01:30:17.137Z
Answers.UserDisplayName: vkkodali
Body: <p>If I go <a href="https://www.ncbi.nlm.nih.gov/nuccore/BA000005.3" rel="nofollow noreferrer">to ncbi site</a>, apply <code>customize view -&gt; Customize -&gt; All features -&gt; Update view</code> and then <code>ctrl + f : Alu</code> I can get all alu repeaing regions coordinates from this chromosome.</p>
  <p>It looks like:</p>
  <pre><code> repeat_region   complement(37490..37800)
                   /note=&quot;AluY&quot;
                   /rpt_family=&quot;SINE/Alu&quot;
                   /rpt_type=DISPERSED
  </code></pre>
  <p>How could I download all this coordinates and names of repeating regions from the internet to .txt file? Or some tool</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-08T12:40:38.827Z
Comments.Text: Hi @WhoAmI, an `efetch` command would be the best option. You can Blast them out ... but the genomic position might not follow (not sure).
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-08T12:58:53.720Z
Comments.Text: @Michael could you write usage example?
Comments.UserDisplayName: WhoAmI
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-08T13:03:35.787Z
Comments.Text: Have a go yourself, thats the best way to get help on site. I don't work on human genomics so its not something I'd do ... but fishing out bits of Genbank annotation is certainly an `efetch` thing.
Comments.UserDisplayName: M__
Tags: <fasta>
Title: How do I get repeating regions from fasta file or directly from internet
ThreadText: # How do I get repeating regions from fasta file or directly from internet
  
  (Asked by: username_0 on 2020-07-08)
  
  If I go [to ncbi site](https://www.ncbi.nlm.nih.gov/nuccore/BA000005.3), apply `customize view -> Customize -> All features -> Update view` and then `ctrl + f : Alu` I can get all alu repeaing regions coordinates from this chromosome.
  
  It looks like:
  
  ```
   repeat_region   complement(37490..37800)
                   /note="AluY"
                   /rpt_family="SINE/Alu"
                   /rpt_type=DISPERSED
  
  ```
  
  How could I download all this coordinates and names of repeating regions from the internet to .txt file? Or some tool
  
  **Tags:** fasta
  
  > **Comments:**
  > **username_1**: Hi @username_0, an `efetch` command would be the best option. You can Blast them out ... but the genomic position might not follow (not sure).  
  > **username_0**: @Michael could you write usage example?  
  > **username_1**: Have a go yourself, thats the best way to get help on site. I don't work on human genomics so its not something I'd do ... but fishing out bits of Genbank annotation is certainly an `efetch` thing.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-07-11. Score: 1
  
  Click on the 'GenBank' dropdown menu at the top left corner of [this page](https://www.ncbi.nlm.nih.gov/nuccore/BA000005.3) to see a [graphical view](https://www.ncbi.nlm.nih.gov/nuccore/BA000005.3?report=graph) of the sequence. You should see a 'Repeat region' track in the Sequence Viewer. Click on the 'Download' button in the top right corner of the Sequence Viewer, choose 'Download Track Data' to launch a dialog box where you can enter a range, select the 'Repeat region' track and download data in BED format. Unfortunately, the names for the features are not great.
  
  If you want the names to be the same ones in the flat file, you can download the feature table and parse it. To download the feature table, click on the 'Send To' link at the top right corner of [this page](https://www.ncbi.nlm.nih.gov/nuccore/BA000005.3), choose 'Complete Record', 'File' and 'Feature Table' as 'Format'. After you download the feature table, you can parse it using `awk` as shown below to create a 4-column table with the data.
  
  ```
  cat seq.ft \
    | awk 'BEGIN{FS="\t";OFS="\t"}{
      if(NF==3) {print s,e,f,q ; s=$1; e=$2; f=$3; q=""} 
      else if(NF==2) {print s,e,f,q ; s=$1; e=$2; q=""} 
      else if(NF==5) {q=q"|"$4"="$5} }' \
    > feat_table.tsv
  
  ```
  
  
  ---
  
  