Questions tagged [genbank]
NCBI sequence annotation flat file.
37
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2
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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 ...
- 75
2
votes
1
answer
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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.
...
- 123
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0
answers
40
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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.
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1
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2
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83
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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....
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2
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2
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145
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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/...
2
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2
answers
144
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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 ...
2
votes
2
answers
440
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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
<...
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3
votes
1
answer
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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 ...
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2
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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 ...
- 131
3
votes
4
answers
363
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 ...
- 387
2
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1
answer
473
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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:
...
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164
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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
- 351
5
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1
answer
364
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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 ...
- 53
0
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0
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42
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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 ...
- 101
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2
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476
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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:
...
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2
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1
answer
69
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How to programmatically classify a protein according to its genbank feature
Say I found an interesting protein in a genbank file, e.g.:
...
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2
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328
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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?
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0
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32
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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 ...
- 307
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0
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87
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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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0
answers
265
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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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1
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1
answer
60
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.
...
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1
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2
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265
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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 ...
- 135
4
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3
answers
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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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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 ...
1
vote
1
answer
70
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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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2
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1
answer
190
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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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4
votes
2
answers
434
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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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1
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0
answers
20
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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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7
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3
answers
1k
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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,
...
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7
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1
answer
401
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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. ...
1
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1
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138
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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 ...
The_Questioner
7
votes
1
answer
86
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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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2
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0
answers
139
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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 ...
- 430
1
vote
1
answer
932
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:
...
3
votes
3
answers
144
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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.
...
3
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1
answer
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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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1
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190
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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 ...
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