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Information


Unique identifier OMICS_06165
Name Transterm
Restrictions to use None
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Transterm

Publication for Transterm

Transterm citations

 (47)
library_books

A Genome Wide Prediction and Identification of Intergenic Small RNAs by Comparative Analysis in Mesorhizobium huakuii 7653R

2017
Front Microbiol
PMCID: 5596092
PMID: 28943874
DOI: 10.3389/fmicb.2017.01730

[…] ) and BPROM 2.4.3.1111 (http://www.molquest.com/). Predictions of Rho-independent terminators were implemented with RNAMotif 3.0.7 (http://casegroup.rutgers.edu/casegr-sh-2.5.html), TransTermHP 2.09 (transterm.cbcb.umd.edu/), FindTerm 2.4.3.1111 (http://www.molquest.com/) and Erpin 5.4 (http://tagc.univ-mrs.fr/erpin/). Searches for known functional RNA sequences among the predicted sRNAs were cond […]

library_books

Effect of acetic acid on ethanol production by Zymomonas mobilis mutant strains through continuous adaptation

2017
BMC Biotechnol
PMCID: 5540488
PMID: 28764759
DOI: 10.1186/s12896-017-0385-y

[…] f reference genome using SAMtools package v.1.19, ZMA-167 had a deletion of 303-bp, which was confirmed using PCR. The deletion truncated 3′ part of ZMO0117 by 255-bp and upstream of ZMO0119 (Fig. ). TransTerm HP search showed that there was a putative ρ-dependent terminator 66 bp downstream of ZMO0117 in ZM481 (HP score is −3.141 and 100% confidence), whereas ZMA-167 had truncated ρ-dependent ter […]

library_books

RNA Seq of Borrelia burgdorferi in Multiple Phases of Growth Reveals Insights into the Dynamics of Gene Expression, Transcriptome Architecture, and Noncoding RNAs

2016
PLoS One
PMCID: 5051733
PMID: 27706236
DOI: 10.1371/journal.pone.0164165

[…] eri B31 genome sequence were performed, then those results were compared with RNA-Seq data. The genome sequence was queried using three separate intrinsic terminator prediction programs: RNAMotif [], TransTerm [], and FindTerm [], as implemented in the SIPHT pipeline []. If a potential terminator was identified any of these programs, it was included for further analysis. Each of these predictions […]

library_books

Genomics of Three New Bacteriophages Useful in the Biocontrol of Salmonella

2016
Front Microbiol
PMCID: 4837284
PMID: 27148229
DOI: 10.3389/fmicb.2016.00545

[…] op codons. Potential promoter regions and transcription terminators were predicted using the Softberry programs BProm (http://linux1.softberry.com/berry.phtml), FindTerm (Solovyev and Salamov, ), and TransTerm (Ermolaeva et al., ). The presence of a putative Shine-Dalgarno sequence (ribosome binding site, RBS) was confirmed based on its similarity to the Escherichia coli consensus sequence GGAGGT […]

library_books

Bacterial small RNAs in the Genus Rickettsia

2015
BMC Genomics
PMCID: 4683814
PMID: 26679185
DOI: 10.1186/s12864-015-2293-7

[…] ntity (BLAST % identity) were set at the default 0. The maximum BLAST high-scoring segment pairs (HSP) length was set at 1000. The maximum Rho-independent terminator criteria were 86, -10, and -6 for TransTerm, FindTerm, and RNAMotif, respectively. The minimum predicted locus length was 30, while the maximum predicted locus length was 550. These scores take into account the generally defined 50 to […]

call_split

RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes

2015
RNA Biol
PMCID: 4829319
PMID: 26580233
DOI: 10.1080/15476286.2015.1110674
call_split See protocol

[…] that start within a window of 11 nt (5 nt upstream and downstream of the sRNA 5' end) should start at that position. Predicted Rho-independent terminators by TransTermHP v2.07 (downloaded from http://transterm.cbcb.umd.edu/tt/Streptococcus_pyogenes_M1_GAS.tt) were analyzed. […]

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Transterm institution(s)
Biochemistry Department and Webster Centre, University of Otago and Bioinfotools, Dunedin, New Zealand

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