Find all genes having ATTAGTTAA in their 3'UTRs

Question

[manu.tiwari]

Hello I want to retrieve gene names/FlybaseIDs of all the Drosophila genes that have a specific sequence (ATTAGTTAA) in their 3'-UTRs. Better would also be the number of times they have such repeats. For individual genes, this is very easy to do (download the 3'UTR FASTA and search for the specific sequence). There is, however, no such option for Batch Download.

Can someone kindly suggest a way to solve this issue? Or is there a way to download only the 3'UTRs of all the genes in a single file using Batch Download or something similar?

Thanks and Best Regards M

[Andrzej Zielezinski]

You can download 3'UTR sequences of all genes from flybase FTP server. For example, to download all 3'UTRs from D. melanogaster click on this link.

[manu.tiwari]

Thanks for the link.

Answer 1

[Jean-Karim Heriche]

Use Ensembl and its API.