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Virtual Ribosome specifications

Information


Unique identifier OMICS_24147
Name Virtual Ribosome
Alternative name dna2pep
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data Some DNA sequences.
Input format FASTA,GenBank,TAB
Programming languages Python
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Information


Unique identifier OMICS_24147
Name Virtual Ribosome
Alternative name dna2pep
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data Some DNA sequences.
Input format FASTA,GenBank,TAB
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Version 1.1
Stability Stable
Source code URL http://www.cbs.dtu.dk/services/VirtualRibosome/download.php
Maintained Yes

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Publication for Virtual Ribosome

Virtual Ribosome citations

 (24)
library_books

Plastid Transcript Editing across Dinoflagellate Lineages Shows Lineage Specific Application but Conserved Trends

2018
Genome Biol Evol
PMCID: 5888634
PMID: 29617800
DOI: 10.1093/gbe/evy057

[…] a first draft gDNA assembly. Each gDNA first draft was used as a template to repeat the assembly process and create gDNA second draft assemblies. Final gDNA and mRNA assemblies were translated using Virtual Ribosome () or Geneious. tRNA screens were performed using tRNAScan and ARAGORN (; ). Details for each P. lunula gene, including mapped genomic and transcript reads, as well as the determined […]

library_books

De novo assembly of a transcriptome from the eggs and early embryos of Astropecten aranciacus

2017
PLoS One
PMCID: 5584759
PMID: 28873438
DOI: 10.1371/journal.pone.0184090

[…] The transcript of the mitochondrial gene encoding cytochrome c oxidase subunit I in A. aranciacus (comp182578) was analyzed with Virtual Ribosome [] by use of the mitochondrial codons of echinoderm. After determining the coding region, homologous DNA sequences in other species of starfish were obtained from GenBank. The region […]

library_books

Down regulation of aminopeptidase N and ABC transporter subfamily G transcripts in Cry1Ab and Cry1Ac resistant Asian corn borer, Ostrinia furnacalis (Lepidoptera: Crambidae)

2017
PMCID: 5555102
PMID: 28808417
DOI: 10.7150/ijbs.18868

[…] tBLASTn algorithm (identity cutoffs ≥ 98% over ≥25 amino acids), and consensus transcripts were reconstructed used CAP3 . Derived protein sequence of each CAP3 assembled contig was obtained using the Virtual Ribosome and reading frame adjusted based on BLASTx search of the NCBI nr protein database. In all cases, the nearest ortholog from the model lepidopteran B. mori were downloaded in FASTA for […]

library_books

Molecular phylogeny reveals food plasticity in the evolution of true ladybird beetles (Coleoptera: Coccinellidae: Coccinellini)

2017
BMC Evol Biol
PMCID: 5485688
PMID: 28651535
DOI: 10.1186/s12862-017-1002-3

[…] The coding DNA sequence of each gene was translated to the corresponding amino-acid sequence with the software Virtual Ribosome (version 2.0; []). The amino-acid sequences of each gene (CADMC, CADXM, TOPO, WGL, COI) were aligned using MAFFT (version 7.164b; []) and the original nucleotide sequences were mapped […]

library_books

Diversity and evolution of sex determination systems in terrestrial isopods

2017
Sci Rep
PMCID: 5430756
PMID: 28439127
DOI: 10.1038/s41598-017-01195-4

[…] To establish a set of orthologous genes to be used in phylogenetic analyses, we first translated each transcriptome using Virtual Ribosome (version 1.1). The first translation strategy consisted in keeping the longest contigs starting with a start codon among the 6 possible open reading frames (ORFs) (parameters used: -r […]

library_books

Genetic variation in bitter taste receptor genes influences the foraging behavior of plateau zokor (Eospalax baileyi)

2016
Ecol Evol
PMCID: 4834321
PMID: 27110349
DOI: 10.1002/ece3.2041

[…] Corporation). The variable site information of DNA sequence was counted directly in the MEGA program (Tamura et al. ). The DNA alignments were then translated into AA (amino acid) sequences using the dna2pep program (Python scripts) (Wernersson ), and polymorphic sites were counted using MEGA. The DNA and AA alignments were also imported into DAMBE (Xia ) to identify individuals with the same geno […]

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Virtual Ribosome institution(s)
Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark
Virtual Ribosome funding source(s)
Supported by a grant from The Danish National Research Foundation and The Danish Research Agency.

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