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So I am preparing some documents about Sar-Cov2 and I wanted to illustrate the "definition" of the virus with the DNA sequence. I found this sequence in GenBank.

Now I think I need an explanation about what this sequence described exatly. From y research, I understood:

  • The first part of the text listed genes that had been identified in Sar-Cov2. Each gene would be responsible of a "feature" of the Sars-Cov2.
  • The second part, named "Origin" in the text, is the complete DNA sequence of the virus.

Now my question is: how is one gene from the first linked to the second part? Is there some sort of "stamp" that allows to say: "gene X starts at fifth letter in DNA sequence and ends at tenth"? If yes, is the information in the text from GenBank (link above)?

Example of the pieces of the file:

First part

FEATURES             Location/Qualifiers
     source          1..29903
                     /organism="Severe acute respiratory syndrome coronavirus
                     2"
                     /mol_type="genomic RNA"
                     /isolate="Wuhan-Hu-1"
                     /host="Homo sapiens"
                     /db_xref="taxon:2697049"
                     /country="China"
                     /collection_date="Dec-2019"
     5'UTR           1..265
     gene            266..21555

[...]

Second part

ORIGIN      
        1 attaaaggtt tataccttcc caggtaacaa accaaccaac tttcgatctc ttgtagatct
       61 gttctctaaa cgaactttaa aatctgtgtg gctgtcactc ggctgcatgc ttagtgcact
      121 cacgcagtat aattaataac taattactgt cgttgacagg acacgagtaa ctcgtctatc
      181 ttctgcaggc tgcttacggt ttcgtccgtg ttgcagccga tcatcagcac atctaggttt
      241 cgtccgggtg tgaccgaaag gtaagatgga gagccttgtc cctggtttca acgagaaaac
      301 acacgtccaa ctcagtttgc ctgttttaca ggttcgcgac gtgctcgtac gtggctttgg
[...]
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    $\begingroup$ Your question is, in my opinion, unsuited for this site for several reasons. First it is not self-contained — it requires one to read a document on an external site to understand. Second it is not sufficiently focused — it is, in effect asking for a complete explanation of a datafile format. Third, one could argue that this is not a problem in biology per se (although this is more debatable than my other objections). However, fourth, and most important, you show no evidence of trying to solve the problem yourself by using the extensive documentation on the NCBI website. $\endgroup$
    – David
    Commented Jun 6, 2021 at 20:18
  • $\begingroup$ For the first reason: the linked document is a dna sequence. I cannot "say it in my own words" and reproducing it in the post is useless and decrease readability. Second: no, it is focused on the link between gene and DNA sequence. Third: yes, this could be an objection. Fourth: I went into some of this documentation, not all. I did not find something that lighten me about how gene are linked to dna sequence $\endgroup$ Commented Jun 7, 2021 at 16:25
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    $\begingroup$ I think it is not unreasonable to expect you to reproduce examples of the file in question. You obviously have identified the different pieces of the structure of the GenBank file. It would be simple enough to place that at the bottom of your question, if you don't like having it in the middle of the question. $\endgroup$ Commented Jun 12, 2021 at 21:52

1 Answer 1

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In a GenBank format file, the first line of each feature entry gives the location of the feature in the sequence. Consider, for example, the second feature in the linked file:

 5'UTR           1..265

This means that the 5' untranslated region of the viral genome is from bases 1 through 265.

Bases start counting with 1, so down below in the sequence after the ORIGIN, marker, this corresponds with the bases:

        1 attaaaggtt tataccttcc caggtaacaa accaaccaac tttcgatctc ttgtagatct
       61 gttctctaaa cgaactttaa aatctgtgtg gctgtcactc ggctgcatgc ttagtgcact
      121 cacgcagtat aattaataac taattactgt cgttgacagg acacgagtaa ctcgtctatc
      181 ttctgcaggc tgcttacggt ttcgtccgtg ttgcagccga tcatcagcac atctaggttt
      241 cgtccgggtg tgaccgaaag gtaag 

Note also that "feature" means more than just genes, as in the case of this 5'UTR. Any identifiable region of interest in a sequence may be marked with a feature. Take a browse through the Sequence Ontology to see what other sorts of things are likely to be marked as features.

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  • $\begingroup$ Thank you for your answer How strong is the association made between the region of interest and the feature ? Is it made with a test (like supprres the zone and see how the feature evolved?) $\endgroup$ Commented Jun 6, 2021 at 12:40
  • $\begingroup$ @totalMongot You'll have to look at the article that produced the sequence to see how they identified features. Most of these features come from sequence analysis. $\endgroup$
    – Armand
    Commented Jun 6, 2021 at 15:16

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