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Searching for multiple protein sequences in subset of DNA

Hello, my question accounts database filtering when using multiple sequence alignment - suppose I need to look for a homologous sequences to all proteins of some kind (all AA-tRNA sythetases for example) in all rRNAs. I can easily download all sequences for synthetase genes in all organisms and also all rRNA sequences. Also I can probably run a search for synthetase genes in rRNA sequences, but it would be really less painful if I could do that via some kind of online database filtering with computations on the other side. Is there any way to select two subsets of sequences and align them to each other in ensembl or another database?

alignment protein dna filtering
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updated by Biostar Biostar • written by tretyacv • tretyacv

Hello tretyacv!

We believe that this post does not fit the main topic of this site.

This question has been overlooked for some time, but with over 600 views I assume that the question is simply unclear. The reason for that is its confusing use of terms that do not make sense biologically. rRNA is not protein coding, still op wanted to look for homology to protein sequence. Unfortunately it is likely too late for clarification now.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by Michael Dondrup Michael Dondrup

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