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I am analysing Pyrococcus Furiosus DNA sequencing data by considering data published here in NCBI. When I click on "Send to">"Gene Features">"FASTA format" I download a file that has the sequences of genes of this organism but I realized that this file has some sequences that are doubled (that is the sequence is present twice with different identifiers)... is there a way to get a file with all genes annotated and their respective DNA sequences without double sequences and with all sequences in the 5' to 3' direction without reverse complement in a well "ordered" way ? In NCBI (in the link I reported before) it indicates 2,128 genes so I would like a file with all these 2,128 genes annotated and their respective DNA sequences in FASTA format. Do you know if there is an other website or an other place in NCBI in which I can search to get this kind of file?

EDIT: if you follow the path "Send to">"Gene Features">"FASTA format", now it seems that there are just 2,128 genes so this problem is vanished in this case. Anyway, I would appreciate the answer for the future and for the reverse complement gene sequences that are still there.

Thank you very much.

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From this SO post. You can use seqkit to remove duplicate sequences with the command below:

seqkit rmdup -s < sequences.txt > out.fa

The rmdup option removes duplicates, and the -s option calls duplicates on the basis of sequence, ignoring differences in headers.

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  • $\begingroup$ thank you @Throckmorton I will try ! Even if my question was more focus on if it exists some website (in general) that has a FASTA format file with all annotated genes, without double DNA sequences or sequences that are reverse complement etc... so that if I remove the FASTA headers, I would obtain the complete genome DNA sequence $\endgroup$
    – HelpNeederStudent
    Commented Sep 2, 2021 at 13:53
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    $\begingroup$ @Manuela does this species really have nothing but genes in its genome? And all of its genes are unique? In other words, are you sure that concatenating all genes will give you the genome? That seems very unlikely to me, but then I've spent most of my career working on eukaryotes. $\endgroup$
    – terdon ♦
    Commented Sep 11, 2021 at 13:03
  • $\begingroup$ @terdon thank you for the observation ! I assumed it was so... I am not a biologist :) $\endgroup$
    – HelpNeederStudent
    Commented Sep 11, 2021 at 16:41
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    $\begingroup$ Ah, then @Manuela it is almost certainly the case the the genome has a lot of DNA that isn't part of any gene. I don't know archea at all, but if we take human as an example, genes are only around ~5% of the genome. If you want the genome, then look for the genome and not the genes. $\endgroup$
    – terdon ♦
    Commented Sep 11, 2021 at 16:58
  • $\begingroup$ ok @terdon thank you . $\endgroup$
    – HelpNeederStudent
    Commented Sep 11, 2021 at 17:56

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