Question: Where to find canonical versions of 18S sequences?
2
gravatar for Pawel Szczesny
3.4 years ago by
Pawel Szczesny3.2k
Poland
Pawel Szczesny3.2k wrote:

I'm doing an analysis of sequence features in 18S rRNA sequences. I have downloaded data from SILVA database. Unfortunately, typical vertebrate has more than a single 18S sequence. I know that most of them are considered pseudogenes, but unless I check them one by one, there's no way to guess which one is a canonical (reference) version. I have roughly 1000 sequences to verify from 150 organisms, so I'd prefer not to do it by hand.

Where to find or how to identify canonical version of 18S rRNA?

 

databases rrna 18s • 1.3k views
ADD COMMENTlink modified 19 months ago by Alex Bel30 • written 3.4 years ago by Pawel Szczesny3.2k
3
gravatar for Alex Bel
19 months ago by
Alex Bel30
University of Liverpool
Alex Bel30 wrote:

The SSU gene of S. cerevisiae (Z75578) is usually used as canonical to mark start and end positions of V1-V9 regions. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087624 there's table 3 in supplemental materials you need.

ADD COMMENTlink modified 19 months ago • written 19 months ago by Alex Bel30
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