# How do I get repeating regions from fasta file or directly from internet

If I go to ncbi site, apply customize view -> Customize -> All features -> Update view and then ctrl + f : Alu I can get all alu repeaing regions coordinates from this chromosome.

It looks like:

 repeat_region   complement(37490..37800)
/note="AluY"
/rpt_family="SINE/Alu"
/rpt_type=DISPERSED


How could I download all this coordinates and names of repeating regions from the internet to .txt file? Or some tool

• Hi @WhoAmI, an efetch command would be the best option. You can Blast them out ... but the genomic position might not follow (not sure).
– M__
Jul 8, 2020 at 12:40
• @Michael could you write usage example? Jul 8, 2020 at 12:58
• Have a go yourself, thats the best way to get help on site. I don't work on human genomics so its not something I'd do ... but fishing out bits of Genbank annotation is certainly an efetch thing.
– M__
Jul 8, 2020 at 13:03

If you want the names to be the same ones in the flat file, you can download the feature table and parse it. To download the feature table, click on the 'Send To' link at the top right corner of this page, choose 'Complete Record', 'File' and 'Feature Table' as 'Format'. After you download the feature table, you can parse it using awk as shown below to create a 4-column table with the data.
cat seq.ft \
if(NF==3) {print s,e,f,q ; s=$1; e=$2; f=$3; q=""} else if(NF==2) {print s,e,f,q ; s=$1; e=$2; q=""} else if(NF==5) {q=q"|"$4"="\$5} }' \