TranSEQ protocols

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TranSEQ specifications

Information


Unique identifier OMICS_07366
Name TranSEQ
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability No
Maintained No

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TranSEQ in pipelines

 (59)
2018
PMCID: 5797582
PMID: 29441050
DOI: 10.3389/fmicb.2018.00063

[…] extracting the respective clusters of orthologous groups (cog) category., first, nucleotide sequences of all annotated pseudogenes of our three strains were extracted, and six-frame translated using transeq (emboss suite 6.6.0.0, http://emboss.open-bio.org/; rice et al., ) to capture potential protein domains present in different reading frames (due to frameshifts). the translated sequences […]

2018
PMCID: 5894186
PMID: 29636006
DOI: 10.1186/s12864-018-4616-y

[…] occurrences of the pfam [] domains pf05729 (nacht domain) and pf14484 (fish-specific nacht associated domain, fisna) (fig. ). second, we translated the assemblies into all six reading frames with transeq [] and used these to search for the nacht and fisna domains using hmmer []. for all species, the number of domains identified was substantially elevated when scrutinizing the assemblies […]

2018
PMCID: 5923486
PMID: 29652800
DOI: 10.3390/v10040192

[…] in the mafft package [,]. the remainder of the 5′ utr and 3′ utr were aligned by global (i.e., g-ins-i) algorithm implemented in mafft package, while the orf sequence was first translated using the transeq algorithm implemented in the emboss package [], then aligned using the global algorithm described above and reverse translated using the tranalign algorithm implemented in emboss []., initial […]

2017
PMCID: 5379710
PMID: 28376793
DOI: 10.1186/s12864-017-3666-x

[…] sheep reference genome via ncbi genome browser that lay between the defensin of interest and the nearest upstream β-defensin. these chromosomal intervals were then translated via linux based emboss transeq into all six open reading frames. the bovine first exons most closely related to the ovine β-defensin gene of interest were aligned to this translation to find a potential first exon. the new […]

2017
PMCID: 5381639
PMID: 28057730
DOI: 10.1093/gbe/evw302

[…] presence of putative pol orfs. to identify the four key protein domains (ap, rh, rt, and int) of pol orfs included in ltr retrotransposons, we first translated each candidate te into six frames with transeq from the emboss package (), and then searched against pfam hmm and cdd profiles by using rps-blast with stop codons (; ). the profiles included: rvt_1 pf00078, rvt_2 pf07727, rt_ltr cd01647, […]


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TranSEQ in publications

 (210)
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] the cob sequences were detected in genomes using exonerate minimum intron 10 bp, maximum intron 5000 bp and protein2genome model. protein sequences were extracted with emboss 6.6.0.0 extractseq, and transeq code table 3. protein sequences were then aligned using muscle [, ]. sequences downloaded from genbank were zymoseptoria tritici (genbank accessionaap81933), ptt (dq919067.1: <1–18, […]

PMCID: 5923486
PMID: 29652800
DOI: 10.3390/v10040192

[…] in the mafft package [,]. the remainder of the 5′ utr and 3′ utr were aligned by global (i.e., g-ins-i) algorithm implemented in mafft package, while the orf sequence was first translated using the transeq algorithm implemented in the emboss package [], then aligned using the global algorithm described above and reverse translated using the tranalign algorithm implemented in emboss []., initial […]

PMCID: 5894186
PMID: 29636006
DOI: 10.1186/s12864-018-4616-y

[…] often, the contigs only contain a subset of the unitigs, and therefore could contain fewer genes. we translated the unitigs assemblies of melaeg and gm_ca454pb into all six reading frames with transeq [] and searched these with the mhci pfam [] domain pf00129, consisting of alpha 1 and 2, using hmmer []. for cod and haddock, the domain spans two exons, thus we counted occurrences […]

PMCID: 5901166
PMID: 29686839
DOI: 10.1002/ece3.3803

[…] merely the result of sequencing errors)., most analyses were run using mathematica v8 scripts unless otherwise noted. we translated dna sequences to aa sequences using the software program emboss transeq (goujon et al., ; rice, longden, & bleasby, ). we excluded from the analysis sequences that had an unexpected reading frame, apparent frameshift substitutions, or stop codons., three […]

PMCID: 5947664
PMID: 29423949
DOI: 10.1111/tbed.12809

[…] & barton, ). gaps, low coverage regions and tandem repeats were removed, so that all sequences could be compared. the sequences of individual orfs were extracted and then translated using emboss transeq (http://www.ebi.ac.uk/tools/st/emboss_transeq/), and the resulting amino acid sequences were aligned using mafft v. 7.157b (katoh & standley, ). maximum likelihood (ml) phylogenetic trees […]


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