Answers.Body: <p>gi looks like a Genbank Identifier.  You can search for the 10 digit number following gi| at the Genbank website.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-10-31T07:46:05.897Z
Answers.LastActivityDate: 2019-10-31T07:46:05.897Z
Answers.UserDisplayName: Jay Moore
Answers.Body: <p>You are looking at the supplementary data of a paper. That seems to have given you a list of features, and some information about those features. Specifically, you seem to have a list of two types of element:</p>
  <ol>
  <li><p>&quot;peg&quot;. Based on the information there, I assume &quot;peg&quot; stands for &quot;protein encoding gene&quot;. Note that all peg lines have a peptide sequence (not seen in your question but present in the original link) and their &quot;function&quot; column is always some sort of protein function (e.g. &quot;hypothetical protein&quot; or &quot;Transposase&quot;).</p>
  </li>
  <li><p>&quot;repeat&quot;. These are presumably <a href="https://www.sciencedirect.com/topics/neuroscience/repeated-sequence-dna" rel="nofollow noreferrer">repetitive elements</a>.</p>
  </li>
  </ol>
  <p>For each line, you are given <a href="https://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html" rel="nofollow noreferrer">an identifier</a> for the sequence in which this element can be found. For example, your first line is on <code>gi|1045318032|gb|MAZB01000333.1|</code>. That is a GI (<code>gi|1045318032</code>) and a GenBank identifier (<code>gb|MAZB01000333.1</code>). If you go to the <a href="https://www.ncbi.nlm.nih.gov/" rel="nofollow noreferrer">NCBI website</a>, and search for <a href="https://www.ncbi.nlm.nih.gov/search/all/?term=1045318032" rel="nofollow noreferrer"><code>1045318032</code></a>, you will find that it is the <a href="https://www.ncbi.nlm.nih.gov/nuccore/1045318032" rel="nofollow noreferrer">Candidatus Erwinia dacicola isolate Erw_SC contig_333, whole genome shotgun sequence</a>.</p>
  <p>So, your first line is telling you that the authors have identified a protein encoding gene on sequence <code>gi|1045318032</code> and the gene starts at position 511 of that sequence and ends at position 2. This might sound odd, but that's because the gene is on the negative (<code>-</code>) strand and positions are calculated with respect to the positive strand. So, if you were to count on the negative, the gene would start at 2 and end at 511.</p>
  <p>The same goes for all the other lines you have there. Just look up the GI number and you can know what sequences they are referring to.</p>
  <p>Finally, the second column, the &quot;feature_id&quot; looks like something specific to this figshare service that is hosting the data. I dont' know what it is, but I would guess it's an identifier for this particular feature. I don't think it has any relevance outside <a href="http://figshare.com" rel="nofollow noreferrer">http://figshare.com</a>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-10-31T12:15:06.283Z
Answers.Text: Thank you very much terdon. This makes sense. Greatly appreciate your kind support.
Answers.UserDisplayName: Dendrobium
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-10-31T11:50:53.467Z
Answers.LastActivityDate: 2019-10-31T15:19:19.193Z
Answers.LastEditDate: 2020-06-18T08:30:41.743Z
Answers.UserDisplayName: terdon
Body: <p>I have no experience in Bioinformatics and I need to understand what the annotations <a href="https://figshare.com/articles/Supp_Tables1-4/8044556/1" rel="nofollow noreferrer">given here</a> mean (I am including the first few lines, please see the link for more):</p>
  
  <pre><code>contig_id                         feature_id              type       location                                 start   stop    strand
  gi|1045318032|gb|MAZB01000333.1|  fig|252393.25.peg.1     peg        gi|1045318032|gb|MAZB01000333.1|_511_2   511     2       -
  gi|1045318033|gb|MAZB01000332.1|  fig|252393.25.repeat.1  repeat     gi|1045318033|gb|MAZB01000332.1|_1_128   1       128     +
  gi|1045318033|gb|MAZB01000332.1|  fig|252393.25.repeat.2  repeat     gi|1045318033|gb|MAZB01000332.1|_318_532 318     532     +
  gi|1045318033|gb|MAZB01000332.1|  fig|252393.25.peg.2     peg        gi|1045318033|gb|MAZB01000332.1|_530_321 530     321     -
  gi|1045318034|gb|MAZB01000331.1|  fig|252393.25.repeat.3  repeat     gi|1045318034|gb|MAZB01000331.1|_1_534   1       534     +
  gi|1045318034|gb|MAZB01000331.1|  fig|252393.25.peg.3     peg        gi|1045318034|gb|MAZB01000331.1|_3_410   3       410     +
  gi|1045318035|gb|MAZB01000330.1|  fig|252393.25.repeat.4  repeat     gi|1045318035|gb|MAZB01000330.1|_1_128   1       128     +
  gi|1045318035|gb|MAZB01000330.1|  fig|252393.25.peg.4     peg        gi|1045318035|gb|MAZB01000330.1|_3_539   3       539     +
  gi|1045318035|gb|MAZB01000330.1|  fig|252393.25.repeat.5  repeat     gi|1045318035|gb|MAZB01000330.1|_413_539 413     539     +
  </code></pre>
  
  <p>Could someone help me to understand what these files and all annotations mean?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-10-31T09:33:49.850Z
Comments.Text: Can you give us some context? Where do you see these? Are they file names, you say? Are these the result of something? The last 4 are different versions of [this whole genome shotgun sequence](https://www.ncbi.nlm.nih.gov/nuccore/1045318032), but I don't recognize the first off the top of my head. Maybe if you could explain more, I would be able to help.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-10-31T11:23:22.393Z
Comments.Text: Thank you terdon. Here are the links to files. I want to understand what is fig| , peg etc https://figshare.com/articles/Supp_Tables1-4/8044556/1   
  
  https://www.biorxiv.org/content/biorxiv/early/2019/03/30/590489/DC3/embed/media-3.xlsx?download=true  https://www.biorxiv.org/content/10.1101/590489v2.supplementary-material?versioned=true  --
Comments.UserDisplayName: Dendrobium
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-10-31T11:32:51.913Z
Comments.Text: Ah, that makes more sense. I have edited your question to include a few lines and the link. Next time, please try to include as much relevant information as you can so we can understand.
Comments.UserDisplayName: terdon
Tags: <file-formats><edger><identifiers>
Title: What do these files / annotations mean?
ThreadText: # What do these files / annotations mean?
  
  (Asked by: username_0 on 2019-10-31)
  
  I have no experience in Bioinformatics and I need to understand what the annotations [given here](https://figshare.com/articles/Supp_Tables1-4/8044556/1) mean (I am including the first few lines, please see the link for more):
  
  ```
  contig_id                         feature_id              type       location                                 start   stop    strand
  gi|1045318032|gb|MAZB01000333.1|  fig|252393.25.peg.1     peg        gi|1045318032|gb|MAZB01000333.1|_511_2   511     2       -
  gi|1045318033|gb|MAZB01000332.1|  fig|252393.25.repeat.1  repeat     gi|1045318033|gb|MAZB01000332.1|_1_128   1       128     +
  gi|1045318033|gb|MAZB01000332.1|  fig|252393.25.repeat.2  repeat     gi|1045318033|gb|MAZB01000332.1|_318_532 318     532     +
  gi|1045318033|gb|MAZB01000332.1|  fig|252393.25.peg.2     peg        gi|1045318033|gb|MAZB01000332.1|_530_321 530     321     -
  gi|1045318034|gb|MAZB01000331.1|  fig|252393.25.repeat.3  repeat     gi|1045318034|gb|MAZB01000331.1|_1_534   1       534     +
  gi|1045318034|gb|MAZB01000331.1|  fig|252393.25.peg.3     peg        gi|1045318034|gb|MAZB01000331.1|_3_410   3       410     +
  gi|1045318035|gb|MAZB01000330.1|  fig|252393.25.repeat.4  repeat     gi|1045318035|gb|MAZB01000330.1|_1_128   1       128     +
  gi|1045318035|gb|MAZB01000330.1|  fig|252393.25.peg.4     peg        gi|1045318035|gb|MAZB01000330.1|_3_539   3       539     +
  gi|1045318035|gb|MAZB01000330.1|  fig|252393.25.repeat.5  repeat     gi|1045318035|gb|MAZB01000330.1|_413_539 413     539     +
  
  ```
  
  Could someone help me to understand what these files and all annotations mean?
  
  **Tags:** file-formats, edger, identifiers
  
  > **Comments:**
  > **username_1**: Can you give us some context? Where do you see these? Are they file names, you say? Are these the result of something? The last 4 are different versions of [this whole genome shotgun sequence](https://www.ncbi.nlm.nih.gov/nuccore/1045318032), but I don't recognize the first off the top of my head. Maybe if you could explain more, I would be able to help.  
  > **username_0**: Thank you username_1. Here are the links to files. I want to understand what is fig| , peg etc https://figshare.com/articles/Supp_Tables1-4/8044556/1     https://www.biorxiv.org/content/biorxiv/early/2019/03/30/590489/DC3/embed/media-3.xlsx?download=true  https://www.biorxiv.org/content/10.1101/590489v2.supplementary-material?versioned=true  --  
  > **username_1**: Ah, that makes more sense. I have edited your question to include a few lines and the link. Next time, please try to include as much relevant information as you can so we can understand.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2019-10-31. Score: 5 | Accepted answer
  
  You are looking at the supplementary data of a paper. That seems to have given you a list of features, and some information about those features. Specifically, you seem to have a list of two types of element:
  
  1. "peg". Based on the information there, I assume "peg" stands for "protein encoding gene". Note that all peg lines have a peptide sequence (not seen in your question but present in the original link) and their "function" column is always some sort of protein function (e.g. "hypothetical protein" or "Transposase").
  2. "repeat". These are presumably [repetitive elements](https://www.sciencedirect.com/topics/neuroscience/repeated-sequence-dna).
  
  For each line, you are given [an identifier](https://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html) for the sequence in which this element can be found. For example, your first line is on `gi|1045318032|gb|MAZB01000333.1|`. That is a GI (`gi|1045318032`) and a GenBank identifier (`gb|MAZB01000333.1`). If you go to the [NCBI website](https://www.ncbi.nlm.nih.gov/), and search for [`1045318032`](https://www.ncbi.nlm.nih.gov/search/all/?term=1045318032), you will find that it is the [Candidatus Erwinia dacicola isolate Erw\_SC contig\_333, whole genome shotgun sequence](https://www.ncbi.nlm.nih.gov/nuccore/1045318032).
  
  So, your first line is telling you that the authors have identified a protein encoding gene on sequence `gi|1045318032` and the gene starts at position 511 of that sequence and ends at position 2. This might sound odd, but that's because the gene is on the negative (`-`) strand and positions are calculated with respect to the positive strand. So, if you were to count on the negative, the gene would start at 2 and end at 511.
  
  The same goes for all the other lines you have there. Just look up the GI number and you can know what sequences they are referring to.
  
  Finally, the second column, the "feature\_id" looks like something specific to this figshare service that is hosting the data. I dont' know what it is, but I would guess it's an identifier for this particular feature. I don't think it has any relevance outside <http://figshare.com>.
  
  > **Comments:**
  > **username_0**: Thank you very much username_1. This makes sense. Greatly appreciate your kind support.  
  
  ---
  
  ### Answer by username_2 on 2019-10-31. Score: 1
  
  gi looks like a Genbank Identifier. You can search for the 10 digit number following gi| at the Genbank website.
  
  
  ---
  
  