transAlign protocols

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transAlign specifications

Information


Unique identifier OMICS_22342
Name transAlign
Alternative name translated alignments
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Perl
Computer skills Advanced
Stability No
Maintained No

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Publication for translated alignments

transAlign in pipeline

2010
PMCID: 2995086
PMID: 20876691
DOI: 10.1093/nar/gkq807

[…] and phrap assemblers whose output is then used for blastn searches against bait sequences and other mitochondrial databases, while alignment is conducted with standard software such as clustal and transalign. these programs can easily be linked up in a pipeline that invokes all steps sequentially without manual intervention. incorrect contigs (as the small number of errors that were resolved […]


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transAlign in publications

 (54)
PMCID: 5775324
PMID: 29352173
DOI: 10.1038/s41598-018-19607-4

[…] selected and labelled mcmv sequences to their region using snps in a 500 bp interval (supplemental table )., to identify protein coding changes within the clades we repeated our ari analysis on translated alignments for each mcmv orf (supplemental tables –). the most significant variation was observed in the coat protein gene and the p7a/p31 region in which the systemic movement protein p31 […]

PMCID: 5754079
PMID: 29300751
DOI: 10.1371/journal.pone.0190511

[…] together with those of the same viruses from the public nucleotide sequence databases using outgroup sequences of nlsyv, jymv, scamv, tumv and wosv. the alignments were made using clustal_x2 [] with transalign (kindly supplied by georg weiller) to maintain the alignment of the encoded amino acids, and the webprank server (http://www.ebi.ac.uk/goldman-srv/webprank/). the nucleotide sequences […]

PMCID: 5749818
PMID: 29299394
DOI: 10.3732/apps.1700079

[…] the dna of the target specimen was degraded and/or the match of primers to template dna was poor. both rbcl and matk sequences were aligned using the back-translation sequence alignment program, transalign, to identify sequences with frameshift mutations (). after filtering out contaminants and correcting editing errors, the sequences were uploaded to bold (www.boldsystems.org)., additional […]

PMCID: 5585334
PMID: 28874826
DOI: 10.1038/s41598-017-11132-0

[…] of the mitochondrial genes identified., the nucleotide sequences of each protein-coding gene were aligned based on codons using the invertebrate mitochondrial genetic code in the perl script transalign. each of trna and rrna genes was aligned using mafft (version 7) under iterative refinement method incorporating the most accurate local (e-ins-i) pairwise alignment information. […]

PMCID: 5604134
PMID: 28922872
DOI: 10.1093/gbe/evx166

[…] each mitochondrion and symbiont were separately aligned using mafft v7.164 b (), using the default parameters. on the basis of amino acid alignment, the nucleotide sequences were aligned using the transalign program in emboss package (). the nucleotide sequences of rrna genes from both the host mitochondria and symbionts were also individually aligned using mafft v7.164 b, with the default […]


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transAlign institution(s)
Lehrstuhl für Tierzucht, Technical University of Munich, Freising-Weihenstephan, Germany
transAlign funding source(s)
Supported by the NGFN-funded project "Bioinformatics for the Functional Analysis of Mam- malian Genomes" (BFAM).

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