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2015 ; 21
(5
): 1005-17
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SRD: a Staphylococcus regulatory RNA database
#MMPMID25805861
Sassi M
; Augagneur Y
; Mauro T
; Ivain L
; Chabelskaya S
; Hallier M
; Sallou O
; Felden B
RNA
2015[May]; 21
(5
): 1005-17
PMID25805861
show ga
An overflow of regulatory RNAs (sRNAs) was identified in a wide range of
bacteria. We designed and implemented a new resource for the hundreds of sRNAs
identified in Staphylococci, with primary focus on the human pathogen
Staphylococcus aureus. The "Staphylococcal Regulatory RNA Database" (SRD,
http://srd.genouest.org/) compiled all published data in a single interface
including genetic locations, sequences and other features. SRD proposes novel and
simplified identifiers for Staphylococcal regulatory RNAs (srn) based on the
sRNA's genetic location in S. aureus strain N315 which served as a reference.
From a set of 894 sequences and after an in-depth cleaning, SRD provides a list
of 575 srn exempt of redundant sequences. For each sRNA, their experimental
support(s) is provided, allowing the user to individually assess their validity
and significance. RNA-seq analysis performed on strains N315, NCTC8325, and
Newman allowed us to provide further details, upgrade the initial annotation, and
identified 159 RNA-seq independent transcribed sRNAs. The lists of 575 and 159
sRNAs sequences were used to predict the number and location of srns in 18 S.
aureus strains and 10 other Staphylococci. A comparison of the srn contents
within 32 Staphylococcal genomes revealed a poor conservation between species. In
addition, sRNA structure predictions obtained with MFold are accessible. A BLAST
server and the intaRNA program, which is dedicated to target prediction, were
implemented. SRD is the first sRNA database centered on a genus; it is a
user-friendly and scalable device with the possibility to submit new sequences
that should spread in the literature.