This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to download the sequences of a gene of all species?

Dear everyone,

How do you download the sequences of a gene of all species? For example, dUTPase is an enzyme existing in almost all organisms. How to download the coding DNA sequences of dUTPase of all organisms? I searched GenBank with the keyword "dUTPase" and it returned 73570 results. Many of these results are complete genome sequences which contains the dUTPase gene. Is there a way to extract only the dUTPase gene sequence from each of the results? Or is there a better way to get the sequences of a certain gene from all species.

Another question is: if I have get sequences of a certain gene from all species, how should I analysis the evolutionary relationship among them? I mean how do I know which sequences are the ancient sequences and which are the progeny ones?

I will be grateful if anyone can help.

Best regards,

Arthur

sequence
• 1,967 views • link
updated by MatthewP MatthewP • written by sunyeping • sunyeping

Which genbank database did you search? You will need to search specifically the 'gene' or 'protein' databases (for instance) else you will usually be given the genome result.

• 0 views • link
written by Joe Joe

1 answer

Hello, as far as I know, e-utils may help you, however if you want to download all species this may require some web scraping skills(I will assume you have). First you get all UIDs for your gene, then get the sequence.

• 0 views • link
written by MatthewP MatthewP

Log in to answer this question.

More posts like this