I have a list of bacteriophage names. A program that I am using would like the GenBank entries for all of these phage.
For instance: http://www.ncbi.nlm.nih.gov/nuccore/339754473
Now, there is the option to download all of these by hand using the Send feature. But is there a second, faster way to do so? I found the Entrez utilities feature, but I'm not sure if that's what I'm looking for. Does anyone have any suggestions?
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written
by
virpatel3 •
2 answers
Parse the accessions from this table and fetch them with entrez direct, e.g.
efetch -db nuccore -id NC_015250 -format gb > NC_015250.gbk
Alternatively something like:
esearch -db genome -query "Acinetobacter phage 133" | elink -target nuccore | efetch -format gb > thisGenome.gbk
Hi
I am building a program that is doing this. Full graphic interface. It will be part of a larger project called NCBI Blaster.
NCBI BLAST DB Downloader and NextGen Workbench will also be integrated into NCBI Blaster.
I will post these day a beta (but functional version).
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