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Protocols

BSRD specifications

Information


Unique identifier OMICS_01533
Name BSRD
Alternative name Bacterial Small Regulatory RNA Database
Restrictions to use None
Data access File download, Browse
User data submission Allowed
Maintained Yes

Maintainer


  • person_outline Hoi Shan Kwan

Publication for Bacterial Small Regulatory RNA Database

BSRD citations

 (7)
call_split

Gene expression of Vibrio parahaemolyticus growing in laboratory isolation conditions compared to those common in its natural ocean environment

2017
BMC Microbiol
PMCID: 5437538
PMID: 28525966
DOI: 10.1186/s12866-017-1030-6
call_split See protocol

[…] position in the reference genome using SAMtools []. Annotation of the V. parahaemolyticus RIMD2210633 genome was done using information in RefSeq [] for open reading frames (ORF), tRNA, and rRNA, and BSRD [] for sRNA with a custom script. Reads counting for each feature were determined using HTSeq-count with the following parameters: -f bam, −r pos, −s reverse, −a 10, −m union []. The overall frag […]

library_books

Genome wide identification and characterization of small RNAs in Rhodobacter capsulatus and identification of small RNAs affected by loss of the response regulator CtrA

2017
RNA Biol
PMCID: 5546546
PMID: 28296577
DOI: 10.1080/15476286.2017.1306175

[…] ere obtained using the batch search functionality in the Rfam database (version 12.1). If an sRNA had multiple Rfam matches only the most significant match was considered. All 30581 sRNA sequences in BSRD were downloaded (May 2015) and a BLAST database was created with these sequences. BSRD matches per sRNA were obtained using blastn with the same settings as for the homology search. If an sRNA ha […]

library_books

Mycoplasma non coding RNA: identification of small RNAs and targets

2016
BMC Genomics
PMCID: 5088518
PMID: 27801290
DOI: 10.1186/s12864-016-3061-z

[…] lar nucleotide composition profile and structural-based features. Known ncRNA sequences of Mollicutes (rRNA, tRNA, RNase P and other functional ncRNAs) were obtained from the Bacterial sRNA Database (BSRD) [] and from the bacterial genome annotation. The genomes used for the new sRNAs search were masked in all regions marked as coding sequence (CDS) in the annotation files of M. hyopneumoniae, M. […]

library_books

Effect of Shear Stress on Pseudomonas aeruginosa Isolated from the Cystic Fibrosis Lung

2016
MBio
PMCID: 4981712
PMID: 27486191
DOI: 10.1128/mBio.00813-16

[…] was predicted by the use of RNAfold (part of the Vienna package []) and only sRNA candidates that were able to form a secondary structure were kept. The sRNAs were aligned against the sRNA entries in BSRD (Bacterial Small Regulatory RNA Database) () with BLAST 2/2/28+ (), but none showed significant homology (i.e., an E value below 0.0001). […]

library_books

High Resolution Transcriptomic Analysis of the Adaptive Response of Staphylococcus aureus during Acute and Chronic Phases of Osteomyelitis

2014
MBio
PMCID: 4278534
PMID: 25538190
DOI: 10.1128/mBio.01775-14

[…] strain 6850 genome sequence using BLAST (). In addition, the small fraction of noncoding mRNA reads (from 0.01 to 7.3% of the total generated reads per library) was further BLAST searched against the BSRD database (http://kwanlab.bio.cuhk.edu.hk/BSRD), where sequence matches of >28 nt with >98% sequence homology and an E value of 0.001 were considered. Raw mapped read counts were then either norma […]

call_split

Comparative genomic analysis of clinical and environmental strains provides insight into the pathogenicity and evolution of Vibrio parahaemolyticus

2014
BMC Genomics
PMCID: 4320434
PMID: 25518728
DOI: 10.1186/1471-2164-15-1135
call_split See protocol

[…] A list of small RNA sequences was retrieved from the BSRD database []. sRNA homologs in our V. parahaemolyticus isolates were then identified using BLASTn. The e-value of BLAST was set to 1e-5. Annotation of CRISPR elements was done using CRISPRfinder [ […]


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BSRD institution(s)
Biology Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China

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Dataset
The Website is clearly arranged, BLAST super fast and the results browser is great.