Questions tagged [genbank]

NCBI sequence annotation flat file.

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How to extract Genbank sequence and identify ORFs from the sequence in R?

I used ape::read.GenBank and then used the function ORFik::findORFs to find ORFs in the sequence of interest. But the former ...
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UTR features in gbk files

I have a gbk files for a viral genome that I have used biopython to add features of the 3' and 5' ...
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GCF VS GCA or combination of both for pangenomic studies

I have just started to learn bioinformatics and pangenomics. So if this question seems to you pretty basic then I apologize in advance. As we know, NCBI for the genome database, there are two kinds of ...
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The best tool to count the number of insertion sequences in a set of bacterial genome

I have a set of 414 GenBank genomes and I need to count a number of insertion sequences (ISs, transposases) in each of them. Is there any traditional way to perform such an analysis? I came up with ...
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How can I retreive specific qualifiers from genbank files in R?

I'm trying to extract the host field from the features table using the biofiles package. From what I understand, the function filter (from the same package) could be of help but I can't extract the ...