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NCBI feature table sequence extraction

Hi ,

I have list of mitochondrial genome accession ids (~100) . There are ways to download entire sequences of these ids (using batch entrez/Efetch or many other options). But i need to download only the feature table sequences (coding genes, trnas and rrnas). I searched efetch option, i could find only to download coding sequences (both aa/nt). Is there a way to download all the feature table sequences directly.

ncbi programming efetch
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updated by Sej Modha Sej Modha • written by Prasad Prasad

Please post a few examples of the ids you have..

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written by 5heikki 5heikki

example ids are CP006559.1, CP006545.1, CP006544.1 etc

• 1 views • link
written by Prasad Prasad

1 answer

You can use Unix eutils for this.

If the sequences are in a text file then write a small bash loop to read the file line by line and run the following command for each accession number. 

for x in $(cat $1)
do
        esearch -db nucleotide -query "$x"|efetch -format ft

don
• 1 views • link
written by Sej Modha Sej Modha

thanks. I will install unix eutils and try

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written by Prasad Prasad

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