Hello Everyone,
I have to do data collection for my current project where i have to collect all the 3' UTR sequences given Ensembl GeneID and Ensembl Transcript ID. I am new to this field and was wondering whether there is an easier way to do this than manually getting each 3' UTR. I have a list of GeneID and Transcript ID.
I did explore Ensembl BioMart, however i could not figure out how to exactly input both GeneID and transcriptID.
Also, would there be a way to incorporate this into python? I do know SQL at Beginner-Intermediate level.
Thank you very much in advance.
A possibly more convenient solution: https://github.com/hammerlab/pyensembl
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alex.rubinsteyn
Biomart: http://www.ensembl.org/biomart/martview
Database: Ensembl Genes 61 Dataset: Homo sapiens genes
Filters: check box on ID list limit There is a text area where you can paste Ensembl gene ids, i.e.: ENSG00000139618
Attributes: Sequences
Then below select: 3' UTR
Click count (top left of the page) just for checking, then go for Results.
You do not need to input both GeneID and transcriptID at the same time, the transcript id should be sufficient and it is unique. It is true that a gene can have multiple transcripts, but a transcript should only be assigned to one gene, so with a transcript id, gene ids are redundant.
Biomart has some built in tools to automatize querys, here is an exported URL to a Biomart query, such as the one described by darked, but with transcript ids as a filter instead of Ensembl gene ids. If you follow the link, you have a query you can start with. You can also get this query as XML or directly as a perl script. If you really must use python, there is more documentation on how to use the REST or SOAP interface.
Darked89 and Michael Dondrup: thank you for answering my question
Michael: I tried it the way u suggested. However i only get back 1 result after inputting all my transcript ids. example link with multiple ids a bit shorter
Here is the [file with all the TransID][2]
Thank you for your time.
[2]: http://www.filedropper.com/transid "file with all the transID
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Sam •
No, your link works fine, the result is a multi-fasta file, scroll down ;)
Argh! I realise your reply was too large to paste in as a comment, but please do not add an answer if you're trying to address comments. If you want to paste a large amount of text into a comment on someone else's reply, please use something like http://pastebin.com/ and point a link to the output you would like us to look at!
He tried to do it right, but the very long URL broke the formatting. I put a shorter URL.
Michael: Thank you very very much. I realized after looking at your shortened link that i was not putting commas after every transcript ID. Therefore it was not querying all the ID's. You put in 5 ID's separated by commas and therefore it queried and returned all of them. I put all my ID's in that format and i got the answer! Thank you very much for all your time and effort. :)
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