Entering edit mode
12.7 years ago
Arun
•
0
How to download .gbk files from ncbi website?
How to download .gbk files from ncbi website?
Search for the sequence that you want. The "display settings" link at the upper left hand corner will allow you to display the entry in various formats. Choose genbank. The upper right hand corner has a "send to" button that'll let you send to file and download the entry in genbank format.
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FYI (and anyone else), the NCBI website has extensive help documents, linked to right from their front page. For example: the handbook - http://www.ncbi.nlm.nih.gov/books/NBK3831/, which contains help on the Entrez databases - http://www.ncbi.nlm.nih.gov/books/NBK3836/, where the topic "Displaying and Saving a Set of Records" answers your very question.
This is a much older question but I am having the same issue and have followed the posted answers. NCBI seems to only be providing me with GenBank flat format files not regular gb/gbk, which I need for annotations when importing into MauveAligner.
Please advise.
What does that mean? A GenBank format file will contain annotation but will still be plain text.
For example using EntrezDirect (truncated for space):
the best way to get GenBank files in 2021 is with
bio
then
nothing needs to be set,
bio
will all figure it out. If you want the gff file do:Then use the rest of
bio
to manipulate the file to your hearts content.when the GB file contains more data the format has to be
gbwithparts
otherwise just a skeleton file with top level annotation will be returned.Hi, why did you delete this post, especially after it was replied to?
Thought I had deleted it before anyone replied, I had figured it out, although it was not intuitive.
You could just add what you figured out, especially if it's not intuitive. Other people (including your future self) could benefit from the time you spent addressing this problem.