Question: Amino Acid sequence to Genebank (.gbk)
0
gravatar for connordejager
23 months ago by
connordejager0 wrote:

Hello,

I am trying to run a BRIG analysis for a number of specific bacteriophage genes. I have all the amino acid sequences I need, I just need to put them into a genebank file so the BRIG program can read them.

Thank you for your help, -Connor DeJager

brig protein genebank • 676 views
ADD COMMENTlink written 23 months ago by connordejager0

Why not just download the genbank of the bacteriophage from NCBI?

BRIG lets you have multiple feature tracks so you can just pass it a file of annotations I believe.

Alternatively, I wrote a script to do pretty much exactly this - extract a genbank for a given sequence or coordinate: https://github.com/MicroInfect/bioinfx/blob/master/Genbank_slicer.py

(This is really for nucleic acid as I intended it to be used for slicing operons out of genomes) it could be repurposed easily enough though

Basically, given a genbank record, BioPythons SeqIO has [start:end] notation you can use to subset a genbank and get all the features in bewteen in the process.

ADD REPLYlink modified 23 months ago • written 23 months ago by jrj.healey11k
0
gravatar for genomax
23 months ago by
genomax63k
United States
genomax63k wrote:

Reverse translate using EMBOSS. Convert to GenBank format using Seqret from EMOBSS.

ADD COMMENTlink written 23 months ago by genomax63k

Thanks! I have a couple of questions still, Why do I reverse translate? Seqret can take the protein sequence as input, it doesn't need to be nucleotide. How do I download the file from Seqret as a .gbk? I can only download as a .txt. Thank you for your help

ADD REPLYlink written 23 months ago by connordejager0

Sorry for some reason I thought you wanted to get GenBank format DNA files. You can use a protein sequence and download GenBank/GenPept format file. Genbank files are in text format. You can save that file as .gbk instead of .txt.

ADD REPLYlink written 23 months ago by genomax63k

The only drop down menu option for file type is a text document, and if I add .gbk to the end it just adds .gbk to the filename.

ADD REPLYlink written 23 months ago by connordejager0

Make sure you put your protein sequence in fasta format.

>Identifier
Sequence of protein here

Select Input Format as Fasta and Output format as GenBank. Save the result as `.gbk.

ADD REPLYlink modified 23 months ago • written 23 months ago by genomax63k
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