Exploring Ensembl exercises

 

Finding out about Ensembl species

 

Exercise 1 — Panda

(a) Go to the species homepage for Panda. What is the name of the genome assembly for Panda?

(b) Click on More information and statistics. How long is the Panda genome (in bp)? How many genes have been annotated?

 

Exercise 2 — Zebrafish

(a) What's new in release 90 for zebrafish?

(b) What previous assemblies are available for zebrafish?

 

Exercise 3 — Mosquitos

(a) Go to Ensembl Metazoa. How many species of the genus Anopheles are represented in Ensembl Metazoa?

(b) When was the current Anopheles gambiae genome assembly last revised?

 

Exercise 4 — Bacteria

Go to Ensembl Bacteria and find the species Belliella baltica. How many coding and non-coding genes does it have?

Region in Detail view

 

Exercise 5 — Exploring a genomic region in human

(a) Go to the region from 31,937,000 to 32,633,000 bp on human chromosome 13. On which cytogenetic band is this region located? How many contigs make up this portion of the assembly (contigs are contiguous stretches of DNA sequence that have been assembled solely based on direct sequencing information)?

(b) Zoom in on the BRCA2 gene.

(c) Configure this page to turn on the Tilepath track in this view. What is this track? Are there any Tilepath clones that contain the complete BRCA2 gene?

(d) Export the genomic sequence of the region you are looking at in FASTA format.

(e) Turn off all tracks you added to the Region in detail page.

 

Exercise 6 — Exploring assembly exceptions in human

(a) Go to the region 21:32630000-32870000 in human. What is the red highlighted region? What is its name?

(b) Can you see the assembly exceptions in the chromosome overview at the top? How many regions with assembly exceptions are there on chromosome 21?

(c) Can you compare this assembly exception with the reference? What is different between this assembly exception and the version on the primary assembly?