Below you will find pages that utilize the taxonomy term “ensembl”
Blog
Super Long Introns of Euarchontoglires
There was another weird result I got about my exon/intron boundaries analysis research. To less diverse species’ genes, intron lengths are shown to increase. However, according to my findings, at a point of Euarchontoglires or Supraprimates, this increase is very sharp and seems unexpected. So, I looked at exon/intron length each gene in each taxonomic rank and try to see what makes Euarchontoglires genes with that long introns.
As you see in the graph above, Euarchontoglires introns are very long compared to the rest.
Blog
An Exon of Length 2 Appeared in Ensembl
I want to share an interesting finding about our research on exon/intron analysis of human evolutionary history.
So I had the genes that emerged at each pass point of human history and I was using Ensembl API to get exons and introns of these genes to perform further analyses.
There was one gene (ENSG00000197568 - HERV-H LTR-associating 3 - HHLA3) with a surprise. Because it’s one transcript (ENST00000432224) had an exon (ENSE00001707577) of length 2.
Blog
How to Get Transcripts (also Exons & Introns) of a Gene using Ensembl API
As a part of my project, I need to obtain exons and introns of certain genes. These genes are actually human genes that are determined for a specific reason that I will describe later when I explain my project. But for now, I want to share the way to obtain this information using (Perl) Ensembl API. Note that Ensembl has started a beautiful way (Ensembl REST API) of getting data but it is beta and it doesn’t provide exons / introns information.
Blog
Install Ensembl API and BioPerl 1.2.3 on Your System
I’m going to work on a project that requires lots of queries on Ensembl databases so I wanted to install Ensembl API to begin with. Since it’s programmed in Perl, I will be using Perl in this project.
There is a nice tutorial on Ensembl website for API installation. Here I will describe some steps.
1. Download the API and BioPerl
Go to Ensembl FTP ftp://ftp.ensembl.org/pub/ and download “ensembl-api.tar.gz” or click here