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Number of citations per year for the bioinformatics software tool Bcheck
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Bcheck specifications

Information


Unique identifier OMICS_22636
Name Bcheck
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some DNA or RNA sequences.
Input format FASTA
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainers


  • person_outline Ivo Hofacker
  • person_outline Dilmurat Yusuf

Additional information


http://rna.tbi.univie.ac.at/bcheck/help.html

Publication for Bcheck

Bcheck citations

 (6)
library_books

Horizontal Acquisition and Transcriptional Integration of Novel Genes in Mosquito Associated Spiroplasma

2017
Genome Biol Evol
PMCID: 5726471
PMID: 29177479
DOI: 10.1093/gbe/evx244

[…] the VELVETH kmer length was set to 47 and the additional parameter settings for VELVETG were “-read_trkg yes -exp_cov 4000 -cov_cutoff 400 -min_contig_lgth 100.” The Rfam database (), ARAGORN (), and Bcheck () were used to annotate the resulting contigs. […]

library_books

Origin and evolutionary history of freshwater Rhodophyta: further insights based on phylogenomic evidence

2017
Sci Rep
PMCID: 5462760
PMID: 28592899
DOI: 10.1038/s41598-017-03235-5

[…] RNAs as queries, and transfer RNAs (tRNA) and tmRNA were identified using using the tRNAscan-SE Search Server (http://lowelab.ucsc.edu/tRNAscan-SE/). The ribonuclease P gene (rnpB) was detected using Bcheck online web server. Newly generated organelle genomes were deposited in GenBank. […]

library_books

Comprehensive Insights in the Mycobacterium avium subsp. paratuberculosis Genome Using New WGS Data of Sheep Strain JIII 386 from Germany

2015
Genome Biol Evol
PMCID: 4607514
PMID: 26384038
DOI: 10.1093/gbe/evv154

[…] ncRNAs were annotated by homology search of Rfam (v.11.0) () families using the Genomewide RNA Annotation Pipeline (GORAP) (unpublished data), which currently comprises Infernal (v1.1) (), Bcheck (v0.6) (), RNAmmer (v1.2) (), and tRNAscan-SE (v1.3.1) () for detection of different ncRNA classes. Within the pipeline, family-specific parameters and several filter steps based on taxonomy, s […]

library_books

Defining the transcriptomic landscape of Candida glabrata by RNA Seq

2015
Nucleic Acids Res
PMCID: 4330350
PMID: 25586221
DOI: 10.1093/nar/gku1357

[…] ein-coding RNAs based on the reference genome and the constructed transcriptome assemblies (TRINITY (), CUFFLINKS ()).GORAP uses BLAST (), Infernal v1.1 (), RNAmmer v1.2 (), tRNAscan-SE v1.3.1 () and Bcheck v0.6 (). Additionally, GORAP screens for known non-protein-coding genes provided by the Rfam database v. 11.0 (). After running GORAP, all resulted Stockholm alignments, related FASTA and GFF f […]

library_books

The human gut and groundwater harbor non photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

2013
eLife
PMCID: 3787301
PMID: 24137540
DOI: 10.7554/eLife.01102.024

[…] RnpB RNAs were identified by searching for matches to 5′ GAGGAAAGUCC 3′, which is highly conserved in RNase P RNAs (), as well as the surrounding intergenic region. Matches were analyzed in Bcheck () to determine the structure and type of the RnpB RNAs. […]

library_books

Evolution of Red Algal Plastid Genomes: Ancient Architectures, Introns, Horizontal Gene Transfer, and Taxonomic Utility of Plastid Markers

2013
PLoS One
PMCID: 3607583
PMID: 23536846
DOI: 10.1371/journal.pone.0059001

[…] onservation of N-terminal regions across red algal and red alga-derived plastids. Ribosomal RNA, tRNA and small RNA genes were predicted using RNAmmer 1.2 Server , tRNAscan-SE 1.21 and ARAGORN , and Bcheck rnpB Server , respectively. All updated annotations are available upon request. Group II intron boundaries were predicted according to 5′ and 3′ conserved motifs, and integrity of1 gene sequenc […]


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Bcheck institution(s)
Institute for Theoretical Chemistry, University of Vienna, Wien, Austria; Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marburg, Germany; Bioinformatics Group, Department of Computer Science University of Leipzig, Leipzig, Germany; Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany; Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany; Santa Fe Institute, Santa Fe, NM, USA
Bcheck funding source(s)
Supported by the Austrian GEN-AU projects “bioinformatics integration network III”, and in part supported by Landesstipendium Sachsen.

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