Where to find canonical versions of 18S sequences?
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6.4 years ago

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?

 

rrna 18S databases • 2.1k views
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4.6 years ago
Alex Bel ▴ 30

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.

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