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ConsPred specifications

Information


Unique identifier OMICS_12364
Name ConsPred
Software type Application/Script, Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, Perl, Shell (Bash)
Computer skills Advanced
Stability Stable

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Maintainer


This tool is not maintained anymore.

Information


Unique identifier OMICS_12364
Name ConsPred
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, Perl, Shell (Bash)
Parallelization MapReduce
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline Thomas Rattei <>

Publication for ConsPred

ConsPred in publications

 (4)
PMCID: 5240343
PMID: 28094312
DOI: 10.1038/srep40455

[…] and all prebin-sequences. quality of sequence binning was evaluated with checkm. gene prediction and functional annotation of predicted protein sequences within each bin were computed using conspred (https://sourceforge.net/projects/conspred/) with uniprot, swissprot and trembl as reference databases and consistently annotated functions were identified for each of the predicted gene […]

PMCID: 5322300
PMID: 27983719
DOI: 10.1038/ismej.2016.148

[…] putative origin of replication was set with genskew (http://genskew.csb.univie.ac.at/). synteny and rearrangements between genomes were visualized by mauve ()., we used an in-house pipeline, called conspred (weinmaier et al., unpublished; available at https://sourceforge.net/p/conspred/) for gene prediction and annotation. detailed description of the annotation method is available in the . […]

PMCID: 4897800
PMID: 27279900
DOI: 10.1186/s13068-016-0534-x

[…] amphora2 results by determining the consensus lineage of all bin-specific marker genes (cut-off confidence scores >0.8). annotation of the genome bins was performed using the annotation framework conspred v1.21 (http://sourceforge.net/p/conspred/wiki/home/). in the file “conspred_input_specification.txt”, the parameters “taxon exclude”, “minimal number rrna”, and “minimal number trna” […]

PMCID: 4428218
PMID: 26029184
DOI: 10.3389/fmicb.2015.00440

[…] strains. afterwards, the phylogenetic tree was computed with geneious 8.0 (kearse et al., ) using 1000 runs for bootstrapping., gene prediction and annotation were obtained from the in-house conspred workflow. conspred consists of two phases: ab initio as well as homology-based predictions. ab initio predictions are followed by genemark.hmm (lukashin and borodovsky, ), glimmer (delcher […]

ConsPred institution(s)
Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria; Department of Microbiology, Radboud University Nijmegen, Nijmegen, Netherlands; Department of Genome Oriented Bioinformatics, Technische Universität München, Freising, Germany

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