Bcheck statistics

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Associated diseases

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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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Maintainers


  • person_outline Ivo Hofacker <>
  • person_outline Dilmurat Yusuf <>

Additional information


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

Publication for Bcheck

Bcheck in publications

 (4)
PMCID: 5726471
PMID: 29177479
DOI: 10.1093/gbe/evx244

[…] 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., for each sample, 5 µg of total rna was reverse transcribed using random hexamers (invitrogen, usa) and the superscript iii first-strand […]

PMCID: 4607514
PMID: 26384038
DOI: 10.1093/gbe/evv154

[…] strains., 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were annotated by homology search of rfam (v.11.0) () families using the genomewide rna annotation pipeline (gorap) (unpublished data), which currently comprises infernal (v1.1) (), bcheck (v0.6) (), rnammer (v1.2) (), and trnascan-se (v1.3.1) () for detection of different ncrna classes.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, […]

PMCID: 4330350
PMID: 25586221
DOI: 10.1093/nar/gku1357

[…] 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 […]

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., the following four genomes were used for the metabolic analyses: acd20, mel.a1, mel.b1, and mel.b2. two partial genomes (mel.a2 […]


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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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