I have a list of more than 400 taxa (species level) of fish for which I want retrieve Genbank sequences with (complete or partial) 12S and COI gene.
I can download each taxa sequences for each gene manually but it's time consuming. I think there are ways to automate this query . Is there anybody that can advice me for such procedure ?
Thank in advances
If you're familiar with Linux command line, you can make a script:
#!/bin/bash
list=`cat $1`
for i in $list
do wget -O $i.fa https://www.ncbi.nlm.nih.gov/search/api/sequence/$i/?report=fasta
done
and then run it ./script.sh list
where 'list' is the file with IDs of sequences.
Dear Emanuel,
I suggest you to see links and attached file on topic.
https://www.biostars.org/p/10959/
https://academic.oup.com/nar/article/43/D1/D1086/2438106
https://www.pnas.org/content/116/45/22651
Best regards
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