RevTrans protocols

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RevTrans specifications

Information


Unique identifier OMICS_03741
Name RevTrans
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No

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Information


Unique identifier OMICS_03741
Name RevTrans
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained No

Maintainer


This tool is not available anymore.

Publication for RevTrans

RevTrans in pipelines

 (2)
2012
PMCID: 3442193
PMID: 23049534
DOI: 10.3389/fpls.2012.00214

[…] sequences inferred from type i and type ii mads-box genes were aligned separately using probcons (do et al., ). protein sequence alignments were reverse translated into nucleotide alignments using revtrans (wernersson and pedersen, ). in the case of type i genes, only the mads-box regions, and in the case of type ii genes, the mads- and the k-box regions, were used for phylogenetic analyses. […]

2009
PMCID: 2764843
PMID: 19865479
DOI: 10.1371/journal.pone.0007666

[…] . multiple sequence alignment of amino acids was performed using the probcons server available from the max plank institute for developmental biology (http://toolkit.tuebingen.mpg.de/probcons). the revtrans 1.4 server (http://www.cbs.dtu.dk/services/revtrans/) was then used to translate the amino acid alignment back into the original dna sequence ., phylogenetic analysis was carried […]


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RevTrans in publications

 (90)
PMCID: 5938362
PMID: 29765366
DOI: 10.3389/fmicb.2018.00854

[…] for mammalian ocln, cd81, cldn1, and scarb1 (encoding srb1) were retrieved from the ncbi database. a list of species is available in the supplementary table . dna alignments were performed with the revtrans 2.0 utility, mafft v6.240 as an aligner) (), which uses the protein sequence alignment as a scaffold for constructing the corresponding dna multiple alignment. all alignments were screened […]

PMCID: 5923437
PMID: 29565808
DOI: 10.3390/v10040143

[…] (ns) proteins and viral proteins (vps), identified in the present study with representative members of the parvovirinae subfamily []. multiple sequence alignment (msa) was carried out using revtrans 2.0 [] with manual adjustment. the alignments of the core of the ns and vp protein ml trees were inferred using iq-tree version 1.4.3 software based on an lg+f+g4 protein substitution model […]

PMCID: 5904367
PMID: 29675140
DOI: 10.3897/CompCytogen.v12i1.20334

[…] and amongst the most and least frequent ltr-retrotransposons in a. duranensis and a. ipaensis genomes. dna corresponding to the sequence coding for the reverse transcriptase enzyme of re128-84 (revtrans-re) and pipoka (revtrans-pip) were used to obtain the probes for fish. since athena family comprises non-autonomous elements, there is no dna sequence coding for the reverse transcriptase […]

PMCID: 5837148
PMID: 29410449
DOI: 10.1038/s41426-017-0009-6

[…] of highest coverage with a minimum alignment length of 300 bp. this region corresponded to reg-2-short, with an alignment length of 360 nucleotides., alignments of all regions were generated using revtrans 2.0, which uses the protein alignment as a scaffold to build the nucleotide alignment., for the phylogeographic analysis of complete hev genomes, sequences were assigned to continents. […]

PMCID: 5847163
PMID: 29143187
DOI: 10.1007/s11262-017-1521-4

[…] corresponding to the four polymorphic loci obtained from genbank. translation of the nucleotide sequences to amino acid sequences for the thymidine kinase and b602l genes was performed using the revtrans 2.0 software []. alignment of the amino acid sequences was then effected using the sequence alignment publishing tool (seqpublish) available in the hiv sequence database with the aim […]


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RevTrans institution(s)
Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark

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