Jump to content

  • Log in with Facebook Log in with Twitter Log in with Windows Live Log In with Google      Sign In   
  • Create Account

Submit your paper to J Biol Methods today!
- - - - -

How to retrieve miRNA sequences from Ensemble using their coordinates ?

  • Please log in to reply
1 reply to this topic

#1 mohsamir1984



  • Active Members
  • Pip
  • 20 posts

Posted 18 February 2020 - 12:00 PM

Dear all, 

I am facing a technical issue in miRNA. I want to retrieve the sequences of 500 duck miRNAs from ENSEMBLE database using their coordinates. For example I have a miRNA genomic location named as "KB742382_1_145970_145992", and I want to retrieve the sequence and the name of this miRNAs. Note: duck genome on ensemble are arranged as scaffolds starts with KB. I think two ways exist: 

1. To download a fasta file from ensemble containing the coordinates and sequences, and then I can use R to subset thhis 

2. To download a gff3 file containing the coordinates and the names, then knowing the names of miRNAs or their transcripts, one can match these with a fasta file being downloaded contains names and sequences , then one can get the sequences ? 


How do you think ? Is this is available for ducks ? 

#2 bob1


    Thelymitra pulchella

  • Global Moderators
  • PipPipPipPipPipPipPipPipPipPip
  • 6,694 posts

Posted 01 March 2020 - 06:05 PM

No idea if this is available for ducks. I think both approaches would work so long as you have the information available to you. From R or Python you could also potentially do some webscraping and retrieve the information directly.

Home - About - Terms of Service - Privacy - Contact Us

©1999-2013 Protocol Online, All rights reserved.