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TransTermHP specifications

Information


Unique identifier OMICS_33515
Name TransTermHP
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 2.09
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Carleton Kingsford

Publication for TransTermHP

TransTermHP citations

 (69)
library_books

Comparative Analysis of 37 Acinetobacter Bacteriophages

2017
Viruses
PMCID: 5795418
PMID: 29295549
DOI: 10.3390/v10010005

[…] 1 × 10−3. Matches to pVOG profiles were considered significant at an e-value of ≤ 1 × 10−15 and ≥35% coverage of the profile HMM. Putative rho-independent terminators were predicted using ARNold and TransTermHP v2.0.9, respectively [,]. tRNAScan-SE and ARAGORN were used to predict tRNAs [,].For the identification of orthologous groups of proteins, translated ORF sequences were clustered into grou […]

library_books

Identification of small RNAs abundant in Burkholderia cenocepacia biofilms reveal putative regulators with a potential role in carbon and iron metabolism

2017
Sci Rep
PMCID: 5688073
PMID: 29142288
DOI: 10.1038/s41598-017-15818-3

[…] in Fig. .The mfold web server was used for RNA secondary structure prediction. The Rfam database was used to search for homologues with known function. Rho-independent terminators were predicted with TransTermHP, using the–all-context command line option to predict terminators independently from annotations. Sequence motifs in upstream sequences were searched for using MEME. sRNA homolology search […]

call_split

Small RNA mediated Cry toxin silencing allows Bacillus thuringiensis to evade Caenorhabditis elegans avoidance behavioral defenses

2017
Nucleic Acids Res
PMCID: 5758910
PMID: 29069426
DOI: 10.1093/nar/gkx959
call_split See protocol

[…] linux1.softberry.com/) and Neural Network Promoter Prediction program (http://www.fruitfly.org/seq_tools/promoter.html); while, the Rho-independent transcription terminators were identified using the TransTermHP program (). The IGRs that contained potential promoter or terminator were retained as potential sRNAs. We then scanned the retained IGRs database using the coding region and promoter seque […]

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

[…] services/Promoter/) 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 predict […]

call_split

Small RNA mediated repression of subtilisin production in Bacillus licheniformis

2017
Sci Rep
PMCID: 5516005
PMID: 28720814
DOI: 10.1038/s41598-017-05628-y
call_split See protocol

[…] ons were extracted from the respective genomes and used for a comparative sequence alignment performed with MUSCLE using default parameters.Transcriptional terminators were predicted with the program TransTermHP. Secondary structure predictions were performed using “The Vienna RNA Websuite”. […]

library_books

DprA from Neisseria meningitidis: properties and role in natural competence for transformation

2017
Microbiology
PMCID: 5817196
PMID: 28696187
DOI: 10.1099/mic.0.000489

[…] conducted using mega version 6 []. The Virtual Institute of Microbial Stress and Survival (VIMSS) website was used to predict operons []. BPROM, BDGP and PPP were used for promoter prediction, while TransTermHP was used to predict terminators []. […]

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TransTermHP institution(s)
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
TransTermHP funding source(s)
Supported in part by grants R01-LM06845 and R01- LM007938 from the National Institutes of Health.

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