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Protocols

SRPDB specifications

Information


Unique identifier OMICS_20024
Name SRPDB
Alternative name Signal Recognition Particle Database
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained No

Maintainer


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Publications for Signal Recognition Particle Database

SRPDB citations

 (4)
call_split

An Algorithm for Template Based Prediction of Secondary Structures of Individual RNA Sequences

2017
Front Genet
PMCID: 5641303
PMID: 29067038
DOI: 10.3389/fgene.2017.00147
call_split See protocol

[…] 2 sequences with pairwise sequence similarity within families ranging from 43 to 95% and sequence similarity to the templates of 20–93%. The sequences were downloaded from Rfam (Gardner et al., ) and SRPDB (Andersen et al., ) databases, or when unavailable in the databases, identified using corresponding papers cited in Table and downloaded from Genbank. As templates, the experimentally identifie […]

call_split

Archaea Signal Recognition Particle Shows the Way

2010
PMCID: 2905702
PMID: 20672053
DOI: 10.1155/2010/485051
call_split See protocol

[…] s are available through the links listed in Supplementary Material 2. In addition, the SRP database provides tables of alphabetically and phylogenetically sorted sequences at http://rnp.uthct.edu/rnp/SRPDB/SRPDB.html. […]

library_books

A fast structural multiple alignment method for long RNA sequences

2008
BMC Bioinformatics
PMCID: 2375124
PMID: 18215258
DOI: 10.1186/1471-2105-9-33

[…] equences. The sequences of each multiple alignment were extracted from tRNA, Intron_gpII, 5S_rRNA, and U5 families in the Rfam 5.0 database and the signal recognition particle RNA family (SRP) in the SRPDB database []. Because the dataset did not include consensus secondary structure annotations to the alignments, we used the secondary structure annotations recovered by Kiryu et al. [].Kiryu et al […]

library_books

An enhanced RNA alignment benchmark for sequence alignment programs

2006
Algo Mol Biol
PMCID: 1635699
PMID: 17062125
DOI: 10.1186/1748-7188-1-19

[…] As a result, emerging alignment tools are generally not tested on non-coding RNA (ncRNA), despite the availability of rather reliable RNA alignments from databases like 5S Ribosomal RNA Database [], SRPDB [], or the tRNA database [].The BRAliBase (Benchmark RNA Alignment dataBase) dataset used in the first comprehensive RNA alignment benchmark published so far [] was constructed using alignments […]

Citations

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SRPDB institution(s)
Department of Molecular Biology, University of Aarhus, C.F. Moellers Allé, Aarhus, Denmark; Department of Medical Biochemistry, Goteborg University, Goteborg, Sweden; SWEGENE Bioinformatics, Goteborg University, Goteborg, Sweden; Danish Genome Institute, Aarhus, Denmark; Department of Natural Sciences, The Royal Veterinary and Agricultural University, Frederiksberg, Denmark; Department of Animal Sciences, Auburn University, Auburn, AL, USA; Center for Bioinformatics and Division of Genetics, IBHV, The Royal Veterinary and Agricultural University, Frederiksberg, Denmark; Department of Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX, USA
SRPDB funding source(s)
Supported by the Interdisciplinary Nanoscience Center (iNANO) of the University of Aarhus, the SWEGENE consortium, the Danish Research Council for Technology and Production Sciences and the Danish Center for Scientific Computing, NIH grants GM-58267 and GM-49034.

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