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Amino Acid sequence to Genebank (.gbk)

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 genebank protein genebank
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written by connordejager • connordejager

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.

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written by Joe Joe

1 answer

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

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written by GenoMax GenoMax

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

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written by connordejager • connordejager

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.

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written by GenoMax GenoMax

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.

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written by connordejager • connordejager

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.

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written by GenoMax GenoMax

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