Skip to main content

Questions tagged [genbank]

NCBI sequence annotation flat file.

Filter by
Sorted by
Tagged with
7 votes
3 answers
2k 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, ...
Alex Summers's user avatar
7 votes
1 answer
438 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. ...
Michael Gruenstaeudl's user avatar
7 votes
1 answer
88 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? ...
Peter Menzel's user avatar
5 votes
1 answer
396 views

KeyError when getting features from a genbank file with biopython with some accessions but not others

I'm very new to python but i've been using it to extract the sequence of a gene from a genbank file. The issue is is that sometimes i'll get the output i want (prints the sequence to a file) and ...
donna's user avatar
  • 53
5 votes
1 answer
347 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 ...
CodeDependency's user avatar
4 votes
3 answers
9k 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 (...
Mark's user avatar
  • 143
4 votes
2 answers
454 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: ...
cmdoret's user avatar
  • 615
4 votes
0 answers
48 views

Linking GenBank records to biosamples (and vice versa) using edirect

Assume that I wish to find all complete human mitochondrial genome records on GenBank (or rather, NCBI nuccore) that also have an entry in NCBI's Biosample database. ...
Michael Gruenstaeudl's user avatar
3 votes
4 answers
450 views

How to programatically download SARS-CoV-2 fasta from NCBI/Genbank via API?

I would like to download a number of SARS-CoV-2 fastas from NCBI/Genbank using a web endpoint. I looked on their website but it's confusing. I have the accession numbers, but can't figure out how to ...
Cornelius Roemer's user avatar
3 votes
1 answer
3k 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 ...
Cleb's user avatar
  • 743
3 votes
2 answers
78 views

What is the best Query to retrieve DNA from NCBI?

I want to retrieve a sequence for many species from the Nucleotide database in NCBI. I'm using a command line approach and I have to figure out what is the best query that will return exclusively the ...
Mirko's user avatar
  • 267
3 votes
1 answer
79 views

What does this accession NCBI code mean: 6MWN_B?

According to this article, accession codes should consist from a combination of uppercase letters following a combination of digits. If this is a RefSeq, it can have a prefix as a combination of ...
Vovin's user avatar
  • 435
3 votes
3 answers
149 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. ...
Aron van Beelen's user avatar
3 votes
0 answers
33 views

Template files for bioattributes and meta-data [closed]

I am in process of submiting my FASTQ files to the SRA database. I am a little confused about how to fill the biosample attributes and SRA metadata. I would really appreciate if you anyone could share ...
Riya's user avatar
  • 307
2 votes
2 answers
207 views

Get genome coordinates from UniProt entry?

I'm trying to get genome coordinate information programmatically for multiple genes. As an example, I'd like to get the annotation (list of exons and their chromosomes, starts, and ends) for this ...
Michael Dunne's user avatar
2 votes
2 answers
597 views

Parsing a genbank file and outputting specific feature information to a csv using BioPython

So I am trying to parse through a genbank file, extract particular feature information and output that information to a csv file. The example genbank file looks like this: SBxxxxxx.LargeContigs.gbk <...
Joe_G's user avatar
  • 101
2 votes
2 answers
184 views

How to properly annotate sequence variants and errors in a GenBank file format and how to keep track of successive versions of a GenBank file

EDIT By thinking over the issue, I realized it was mixing two linked but separate questions: Q1. How to handle the situation when there are divergences between a GenBank file and an actual or ...
The Quark's user avatar
  • 131
2 votes
1 answer
558 views

Entrez (Biopython) esearch and efetch not returning sequence as expected

I'm trying to use Entrez (through Biopython) to download the sequence of a TMV replicase gene. I have the following code: ...
blammo69's user avatar
2 votes
1 answer
69 views

How to programmatically classify a protein according to its genbank feature

Say I found an interesting protein in a genbank file, e.g.: ...
Oren Milman's user avatar
2 votes
1 answer
47 views

BioPython SeqIO fails with Invalid Alphabet found

I am trying to store a GenBank file that could be read by Geneious later. I found an example how to create the GenBank file here But now I run into Alphabet issues. ...
El Dude's user avatar
  • 195
2 votes
1 answer
210 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: ...
Wolfgang's user avatar
2 votes
2 answers
182 views

How do i search by these gene properties in NCBI's GenBank?

I want to search GenBank entries by gene product and taxon id. Taking the 16s rRNA as an example for a gene and Piscirickettsia salmonis (taxon:1238) for a taxon: https://www.ncbi.nlm.nih.gov/nuccore/...
Freezing Soul's user avatar
2 votes
0 answers
145 views

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 ...
Prradep's user avatar
  • 410
1 vote
1 answer
161 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 ...
user avatar
1 vote
2 answers
177 views

How to reverse complement a genbank file?

I am visualizing the alignment of a particular genomic region across different genomes with mauve. In certain genomes the region of interest is in the negative strand and in others the positive strand....
venkatesh war's user avatar
1 vote
2 answers
594 views

Convert sequence in MS doc to fasta or genbank

How can I convert a sequence provided in a Microsoft doc file into a fasta or genbank format?
Peter's user avatar
  • 2,634
1 vote
1 answer
64 views

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. ...
Shadi's user avatar
  • 113
1 vote
2 answers
292 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 ...
karel's user avatar
  • 135
1 vote
1 answer
71 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 ...
JoeT's user avatar
  • 21
1 vote
0 answers
181 views

Convert genbank file into tbl file [closed]

I want to submit some phage sequences to NCBI. So I want to transform a genbank file into a tbl file. Can someone help me please? Thanks
Sofia's user avatar
  • 351
1 vote
0 answers
88 views

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' ...
Lamma's user avatar
  • 175
1 vote
0 answers
347 views

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 ...
Furqan's user avatar
  • 87
1 vote
0 answers
20 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 ...
Some student's user avatar
1 vote
1 answer
1k 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: ...
Aron van Beelen's user avatar
0 votes
2 answers
527 views

Splitting a GenBank file into smaller files

I have a genbank file that I have been trying to run in HMMER using the following command: ...
BhushanDhamale's user avatar
0 votes
0 answers
44 views

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 ...
Lumimoto's user avatar
  • 101
-1 votes
1 answer
219 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 ...
AudileF's user avatar
  • 955