Script to thousands of exons

Sofia Silva · 12-07-2017, 09:43 AM

Hi!

I'm not an expert on informatics so i thought some of you may be able to help me...
I have a list of about 5000 genes and i want to download only the exons of each of them (maybe through ensembl site). It's too much to do it "by hand" and i really don't have that time.
Do you have any idea of how could i do it? Any script that could help me with this?

Thank you in advance for all the attention
Best regards,
Sofia

GenoMax · 12-07-2017, 10:25 AM

No script should be needed. Use BioMart to do this yourself.

Go to Ensembl. Click on BioMart link at the top. A new page should open. Going to show an example for human genome. Hopefully genome of your interest is in BioMart.

1. Choose DB --> Ensembl Genes
2. Choose Dataset --> Human (as example)
3. Click on Filters in left column. Many choices open up on right. Choose what you need
4. Checking Source --> Ensembl for this example
5. Click on the Attributes in left pane
6. Select Sequence button in right pane
7. Expand "Sequences" options by clicking on + sign
8. Select "Exon sequences" radio button
9. Expand "Header Information" by clicking on + sign. Select options as needed
10. Click on the "Count" button at top left corner (e.g. 6460 / 63967 Genes)
11. Hit "Results" button next to count.
12. Use "Export results to file" --> "Fasta"
13. Click on "Go" to download the file (choose unique only if you want that).
14. You are done!

Sofia Silva · 12-07-2017, 10:50 AM

Thank you SO much!!!

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12-07-2017, 09:43 AM	#1
Sofia Silva Junior Member Location: Portugal Join Date: Nov 2017 Posts: 5	Script to thousands of exons Hi! I'm not an expert on informatics so i thought some of you may be able to help me... I have a list of about 5000 genes and i want to download only the exons of each of them (maybe through ensembl site). It's too much to do it "by hand" and i really don't have that time. Do you have any idea of how could i do it? Any script that could help me with this? Thank you in advance for all the attention Best regards, Sofia

12-07-2017, 10:50 AM	#3
Sofia Silva Junior Member Location: Portugal Join Date: Nov 2017 Posts: 5	Amazing! Thank you SO much!!!

12-07-2017, 10:25 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 6,698	No script should be needed. Use BioMart to do this yourself. Go to Ensembl. Click on BioMart link at the top. A new page should open. Going to show an example for human genome. Hopefully genome of your interest is in BioMart. 1. Choose DB --> Ensembl Genes 2. Choose Dataset --> Human (as example) 3. Click on Filters in left column. Many choices open up on right. Choose what you need 4. Checking Source --> Ensembl for this example 5. Click on the Attributes in left pane 6. Select Sequence button in right pane 7. Expand "Sequences" options by clicking on + sign 8. Select "Exon sequences" radio button 9. Expand "Header Information" by clicking on + sign. Select options as needed 10. Click on the "Count" button at top left corner (e.g. 6460 / 63967 Genes) 11. Hit "Results" button next to count. 12. Use "Export results to file" --> "Fasta" 13. Click on "Go" to download the file (choose unique only if you want that). 14. You are done!