User: Salsabil

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Posts by Salsabil

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Comment: C: Virus core genome
... Update: I ended up retrieving GFF3 annotation files directly from NCBI, so the annotation problem is solved at this point. But I'm still getting 0 cores genes in roary results which I don't understand. Because these viruses share most of their genes (if not all of them)! ...
written 29 days ago by Salsabil 0
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Comment: C: Virus core genome
... Exactly, I was expecting a potentially high number of core genes. Especially that these viruses are from the same genus (HIV and SIV). As for the reason I want to work with core genome rather than whole genome, it's because those are highly mutable viruses. ...
written 4 weeks ago by Salsabil 0
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Comment: C: Virus core genome
... Thanks for your feedback. Actually, I found out that when genomes are smaller than 100kb, prokka puts prodigal in "meta" mode automatically. But then, it switches translation tables from 1 (the standard table) to 4. As a result, annotation differs, it doesn't detect all CDS within the genome. For on ...
written 4 weeks ago by Salsabil 0
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Virus core genome
... Hello everyone. I'm working on a bunch of small viral genomes, and I need to construct their core genomes for a comparative study. I've tried using prokka and roary to do so, but since my sequences are too small ( 10 kb or less). I keep getting errors and warnings even though I obtain an output, a ...
genome assembly core-genome sequence virus written 4 weeks ago by Salsabil 0 • updated 4 weeks ago by Mensur Dlakic7.2k
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Virus Multilocus Sequence Analysis(MLSA)
... Hi everyone. This is my first time working on a Multilocus sequence Analysis for a virus. Usually, this technique is based on housekeeping genes in bacteria. But for viruses, I don't know which genes I should focus on. Can anyone please give me some advice concerning this issue. Many thanks! ...
virus mlsa sequencing written 5 months ago by Salsabil 0 • updated 4 months ago by Biostar ♦♦ 20

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