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Consed specifications


Unique identifier OMICS_00879
Name Consed
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Medium
Version 29.0
Stability Stable
Maintained Yes


No version available


  • person_outline David Gordon

Publications for Consed

Consed citations


Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats

Sci Rep
PMCID: 5958079
PMID: 29773850
DOI: 10.1038/s41598-018-26180-3
call_split See protocol

[…] r Biotechnology (CeBiTec) in Bielefeld, Germany. The reads obtained were assembled using GS de novo Assembler software (gs Assembler, version 2.8, Roche). Plasmid finishing was accomplished using the CONSED software package. Complete closed replicons were automatically annotated by the genome annotation system GenDB and manually curated. Genes were annotated using the best BLASTP hit at the Nation […]


Complete and Annotated Genome Sequence of the Sourdough Lactic Acid Bacterium Lactobacillus fermentum IMDO 130101

Genome Announc
PMCID: 5946041
PMID: 29748398
DOI: 10.1128/genomeA.00256-18
call_split See protocol

[…] embler v2.7 with default parameters, followed by gap closure with PCR and Sanger sequencing of the resulting amplicons (VIB Genetic Service Facility, Antwerp, Belgium) based on primers designed using Consed v23.0 (). The starting point of the closed circular genome was repositioned to match the starting point of a representative genome of L. fermentum to facilitate further comparative genomics. Th […]


Elucidation of the anti hyperammonemic mechanism of Lactobacillus amylovorus JBD401 by comparative genomic analysis

BMC Genomics
PMCID: 5918772
PMID: 29695242
DOI: 10.1186/s12864-018-4672-3

[…] lovorus JBD401 (KCTC 11515BP) genome was sequenced by next-generation sequencing using 454 (454 GS FLX) and Illumina methods. Initially, 454 DNA reads were assembled into contigs with the PHRED/PHRAP/CONSED [] software package and subcontracted to Macrogen Inc. Further contigs were assembled using Geneious pro.5.5 software [] and CLC workbench software (CLC Bio-Qiagen). Mapping of assembled contig […]


Genome Guided Analysis of Clostridium ultunense and Comparative Genomics Reveal Different Strategies for Acetate Oxidation and Energy Conservation in Syntrophic Acetate Oxidising Bacteria

PMCID: 5924567
PMID: 29690652
DOI: 10.3390/genes9040225

[…] folding of the selected assembly was performed using SSPACE [] and the removal of possible gaps present in scaffolds was performed using GapFiller []. Homopolymer errors were corrected manually using Consed []. The purity of the scaffolds was also checked against the genome of T. aegyptius DSM 12793. Possible miss-assemblies were corrected manually using Tablet, a graphical viewer for the visualis […]


Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

Environ Microbiol
PMCID: 5900883
PMID: 29327410
DOI: 10.1111/1462-2920.14043

[…] s shreds were integrated, the Illumina VELVET consensus shreds and the read pairs in the 454 paired end library using parallel phrap, version SPS – 4.24 (High Performance Software, LLC). The software Consed (Ewing et al., ; Ewing and Green, ; Gordon et al., ) was used in the following finishing process. Illumina data were used to correct potential base errors and increase consensus quality using t […]


Zinc Deficiency‐Like Syndrome in Fleckvieh Calves: Clinical and Pathological Findings and Differentiation from Bovine Hereditary Zinc Deficiency

PMCID: 5866964
PMID: 29424482
DOI: 10.1111/jvim.15040
call_split See protocol

[…] ns was performed on the ABI 3130xl Genetic Analyzer. The Phred/Phrap/Polyphred software suite, , was used for base calling, sequence alignment, and polymorphism detection. Sequences were viewed with Consed. To avoid false results because of DNA desamination, amplification reactions were performed repeatedly. […]

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Consed institution(s)
Department of Molecular Biotechnology, University of Washington, Seattle, WA, USA

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