Questions tagged [genbank]

NCBI sequence annotation flat file.

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Why does the Genbank phylogenetic tree of 4000 sars-cov-2 sequences only display 200 nodes?

I manually selected all 4000 sequences on the 20 pages of the SARS-CoV-2 sequences on genbank here. When I click on Build phylogenetic tree, it only has 200 nodes. ...
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48 views

Parsing a GenBank file with multiple gene entries

Basically a GenBank file consists of gene entries (announced by 'gene') followed by its corresponding 'CDS' entry (only one per gene) like the two shown here below. I would like to extract part of the ...
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2answers
285 views

Existing tool for converting gff3 to genbank (gbk)

I want to convert my gff3 annotation files to genbank format for use in Mauve. I found the seqret tool here https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/ which can perform this task, but my files (...
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1answer
89 views

which NCBI tool is optimized to identify a species from a DNA fragment?

“The Iceman” was a man who lived 5300 years ago and whose body was recovered from an Alpine glacier in 1991. Some fungal material was recovered from his clothing and sequenced. Ice man : found as a ...
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1answer
37 views

Biopython Genbank writer not splitting long lines

I am parsing a csv file of annotated sequences and using Biopython to generate Genbank files for each. I want to add annotations of the sequence features. My output file shows features listed without ...
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1answer
42 views

Parsing specific features from Genbank by label?

I'm trying to parse a Genbank file to find a specific feature. I can pull it out if I know the feature type (e.g. repeat_region). E.g. if I'm looking for this feature: ...
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2answers
137 views

Entrez.efetch returns incomplete genbank records

I am using the biopython Entrez.efetch command to retrieve all features (CDS, mRNA, ...) of some genomes. In this case (NC_014649, Acanthamoeba polyphaga mimivirus), it works as expected: ...
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0answers
14 views

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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3answers
368 views

Importing GFF file with Biopython

Is there a way to import a GFF file for an organism with Biopython in the same way you can for a Genbank file? For example, ...
7
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1answer
175 views

ANY (technical) reason behind submitting sequences to GenBank versus ENA Sequence

The DNA sequence sections of the three INSDC databases (i.e., DDBJ, ENA Sequence and GenBank) are synchronized periodically and strive to keep their stored data as ubiquitously accessible as possible. ...
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1answer
37 views

Genomics: Downloading genomic data from the NCBI Genbank database

I'm taking a genomics course at school, and we have a final project due in a few weeks. Now, I can write bash scripts to sort and analyze the data, etc. However, I'm not quite sure how to actually ...
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1answer
72 views

Source for whole genome comparisons at NCBI Genomes

The NCBI Genomes database has these dendrograms for (presumably) whole genome comparisons for certain species, e.g. Pseudonomas aeruginosa or Escherichia coli. How were these comparisons done? ...
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56 views

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

I have extracted the sequence using the function ape::read.GenBank and found the function ORFik::findORFs to find ORFs in the ...
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1answer
352 views

Extract certain fields using from GenBank file using Bash script

I need to extract certain lines from a GenBank file on Linux. Input file: ...
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3answers
85 views

How to get the product of a CDS

I need the name of the protein in /product="protein_name" using bash commands. Beware, there is a lot of whitespace between lines. ...
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1answer
617 views

How to extract the protein fasta file from a genbank file?

Let's say I have a genbank file, e.g. the one downloaded from here, that contains entries as ...
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1answer
61 views

How do I get the gene order from genbank file using gene names?

I have a list of gene names which I know are present in a genbank file. I want to order these genes based on the order of their presence in the genbank. This should also account for whether they are ...