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I have downloaded my FASTA format files, that have the DNA sequences of the coding region of the genes and the DNA sequence of the complete genome, from NCBI. How can I recognize if these sequences have been assembled or not ?

In particular, I read this paper Genome Sequencing of a Genetically Tractable Pyrococcus furiosus Strain Reveals a Highly Dynamic Genome and I downloaded the sequences that they indicate in Nucleotide sequence accession number where they say:

The fully assembled DNA sequence of COM1 has been deposited in GenBank (accession number CP003685).

I clicked on the link CP003685 and I downloaded the DNA sequences that I mentioned at the beginning by clicking on "Send to", then "Complete Record",then "File" (in Choose Destination), then FASTA (in Format). For the cds file I made the same steps but clicking on "Coding Sequences" and I could do the same to have the sequences of the genes clicking on "Gene Features". But are these sequences assembled? By reading the extract of the article I would say yes... but is there a way to know this from the FASTA files that I downloaded or the NCBI website ?

Moreover, why is it important to know how a sequence has been assembled (so which software has been used) ?

I apologize for my very basic questions and I thank you in advance.

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Genomes are always assemblies. Assembly basically means making a consensus sequence from many partially overlapping readouts. As there is currently no sequencing technology that allows to sequence an entire genome or even an entire chromosome with a single super high fidelity read that is without errors we have to combine several reads to form the consensus which is then the assembly.

Moreover, why is it important to know how a sequence has been assembled (so which software has been used) ?

Tbh, I never cared on how a genome I used was assembled. To be fair I only work with mouse or human, and for people who work with genomes that are not as well curated as these it might indeed matter, but others would need to comment on that, not really my field.

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  • $\begingroup$ Thank you @ATpoint ... so by "consensus" you mean that you find the nucleotide that appears most frequently at each position by looking at the overlapping readouts? Thus when you have a fasta format file that starts, for example, with ">NC_003413.1 Pyrococcus furiosus DSM 3638, complete sequence" and then you have the nucleotides sequence, does it always represent an assemblied genome ? $\endgroup$
    – HelpNeederStudent
    Commented Aug 2, 2021 at 14:29
  • $\begingroup$ I guess so, yes. $\endgroup$
    – user3051
    Commented Aug 3, 2021 at 6:17
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A nucleotide sequence may be a part of a genome assembly. If so, just click the assembly link from the right panel and you'll be redirected to the assembly page. enter image description here In this assembly page, it says the assembly only contains one chromosome. enter image description here Assembly method is also available for some assemblies. enter image description here

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