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 in publications

 (2)
PMCID: 4834321
PMID: 27110349
DOI: 10.1002/ece3.2041

[…] 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 […]

PMCID: 3733422
PMID: 22839506
DOI: 10.1186/1471-2148-12-129

[…] in mafft [], except for coi, which was aligned using mafft(−einsi) for improved accuracy. to further improve alignment accuracy, protein-coding sequences were then reverse transcribed using dna2pep.py, [] and codon-aligned using translatorx [] and revtrans [] to generate final dna alignments that reflected codon positions. lastly, we visually inspected each alignment for frame shift […]


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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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