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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

Versioning


No version available

Documentation


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


No version available

Documentation


Maintainer


  • person_outline Thomas Rattei

Publication for ConsPred

ConsPred citations

 (4)
library_books

Unraveling the microbial processes of black band disease in corals through integrated genomics

2017
Sci Rep
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 […]

library_books

Convergent patterns in the evolution of mealybug symbioses involving different intrabacterial symbionts

2016
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between genomes were visualized by mauve ()., we used an in-house pipeline, called conspred (weinmaier et al., unpublished; available at https://sourceforge.net/p/conspred/) for gene prediction and annotation.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 . […]

library_books

Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies

2016
Biotechnol Biofuels
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” […]

library_books

The genomes of closely related Pantoea ananatis maize seed endophytes having different effects on the host plant differ in secretion system genes and mobile genetic elements

2015
Front Microbiol
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 […]


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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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