NCBI feature table sequence extraction

Question

[Prasad]

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.

[5heikki]

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

[Prasad]

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

Answer 1

[Sej Modha]

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

[Prasad]

thanks. I will install unix eutils and try