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TranslatorX specifications

Information


Unique identifier OMICS_22371
Name TranslatorX
Interface Web user interface
Restrictions to use None
Input data Some nucleotide sequences, protein alignment, genetic code or alignment cleaning.
Computer skills Basic
Version 0.9
Stability Stable
Maintained Yes

Maintainers


  • person_outline Maximilian Telford
  • person_outline Federico Abascal

Information


Unique identifier OMICS_22371
Name TranslatorX
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainers


  • person_outline Maximilian Telford
  • person_outline Federico Abascal

Publication for TranslatorX

TranslatorX citations

 (179)
library_books

The mitochondrial genome of the oribatid mite Paraleius leontonychus: new insights into tRNA evolution and phylogenetic relationships in acariform mites

2018
Sci Rep
PMCID: 5954100
PMID: 29765106
DOI: 10.1038/s41598-018-25981-w

[…] ite taxa (six Parasitiformes and 31 Acariformes, Supplementary Table ) which included only those species with a complete set of 13 PCGs. First, sequences of each PCG were aligned separately using the TranslatorX server (http://translatorx.co.uk ), where MAFFT is used to build the protein alignment. Translation was done under the invertebrate mt genetic code. Additionally, poorly aligned sites were […]

call_split

Complete Genome Sequencing of a Novel Type of Omikronpapillomavirus 1 in Indian River Lagoon Bottlenose Dolphins (Tursiops truncatus)

2018
Genome Announc
PMCID: 5920176
PMID: 29700141
DOI: 10.1128/genomeA.00240-18
call_split See protocol

[…] o late proteins (L1 and L2), and a noncoding control region.Seventy-six PV L1 nucleotide sequences were retrieved from the Papillomavirus Episteme resource (http://pave.niaid.nih.gov/) and aligned in TranslatorX () guided by amino acid translations with the MUSCLE alignment option. Maximum Likelihood phylogenetic analysis performed in IQ-TREE () supported the bottlenose dolphin papillomavirus (BDP […]

call_split

The Zinc Finger Thylakoid Membrane Protein FIP Is Involved With Abiotic Stress Response in Arabidopsis thaliana

2018
Front Plant Sci
PMCID: 5915565
PMID: 29720990
DOI: 10.3389/fpls.2018.00504
call_split See protocol

[…] Multiple sequence alignments (MSAs) were generated with the TranslatorX server () using MAFFT v.7 software () and curated in Jalview v.2.8.0 or Gblocks [standard parameters; (; )] for large amount of data. MSAs were visualized in Jalview v.2.8.0 () and trimmed […]

library_books

Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi

2018
Sci Rep
PMCID: 5897359
PMID: 29651164
DOI: 10.1038/s41598-018-24301-6

[…] The corresponding protein sequences that composed the OG were aligned with MAFFT v7 and a codon alignment for each OG was then created with TranslatorX using the nucleotide CDS sequence and aligned protein data as a guide. MaxAlign v1.1 was used in codon mode to remove poorly aligned sites and sequences. Any taxa removed from the OG by Ma […]

library_books

Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta)

2018
Genome Biol Evol
PMCID: 5888179
PMID: 29635329
DOI: 10.1093/gbe/evy063

[…] Alignments of named chloroplast protein-coding genes were inferred using TranslatorX (), which translates sequences to amino acids, uses MAFFT () to align the amino acid sequences and generates the corresponding nucleotide alignments. Individual gene alignments were manual […]

call_split

Glutamine Codon Usage and polyQ Evolution in Primates Depend on the Q Stretch Length

2018
Genome Biol Evol
PMCID: 5841385
PMID: 29608721
DOI: 10.1093/gbe/evy046
call_split See protocol

[…] study the glutamine codon usage in the orthologs, we followed the same procedure, counting the number of CAA and CAG triplets forming the Q stretches. In this case, we used the standalone version of TranslatorX (), with default parameters, to easily visualize the nucleotide alignments separated by codons.The length of a Q stretch was considered to be stable if at least half of the orthologs had t […]

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TranslatorX institution(s)
Departamento de Biodiversidad y Biologia Evolutiva, Museo Nacional de Ciencias Naturales, Madrid, Spain; Department of Genetics, Evolution and Environment, University College London, London UK

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