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Information


Unique identifier OMICS_29159
Name FindTerm

Taxon


  • Bacteria
    • Escherichia coli

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Publication for FindTerm

FindTerm citations

 (37)
library_books

A novel short L arginine responsive protein coding gene (laoB) antiparallel overlapping to a CadC like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting

2018
BMC Evol Biol
PMCID: 5810103
PMID: 29433444
DOI: 10.1186/s12862-018-1134-0

[…] The region 300 bp downstream of the stop codon of laoB was searched for the presence and folding energy of a ρ-independent terminator using the program FindTerm (Softberry) []. […]

library_books

A seven gene cluster in Ruminiclostridium cellulolyticum is essential for signalization, uptake and catabolism of the degradation products of cellulose hydrolysis

2017
Biotechnol Biofuels
PMCID: 5663094
PMID: 29093754
DOI: 10.1186/s13068-017-0933-7

[…] Nucleotide sequences analysis were performed using BPROM, FindTerm (http://www.softberry.com) or ARNold (http://rna.igmors.u-psud.fr). Amino acid sequence analysis were performed using on line tools: Signal P, LipoP (http://www.cbs.dtu.dk), BLAST (https://bl […]

library_books

Identification of Trans 4 Hydroxy L Proline as a Compatible Solute and Its Biosynthesis and Molecular Characterization in Halobacillus halophilus

2017
Front Microbiol
PMCID: 5655121
PMID: 29104571
DOI: 10.3389/fmicb.2017.02054

[…] nthetic gene clusters in the genome of H. halophilus were identified using BLASTX and BLASTN and their transcriptional promoters and terminators were predicted using the web-based programs, BPROM and FindTerm, respectively, available at http://www.softberry.com/. […]

library_books

Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome

2017
PLoS One
PMCID: 5597208
PMID: 28902868
DOI: 10.1371/journal.pone.0184119

[…] the novel genes without annotated homologs, respectively ().Transcription termination mediated by ρ-independent terminators [] in the region 300 bp downstream of the stop codon was investigated using FindTerm. For 20.8% of the novel genes with annotated homologs a terminator was predicted. For those without annotated homologs, the fraction was slightly lower (). […]

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

[…] tp://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 conducted within the Rfam data […]

library_books

Isolation and Characterization of phiLLS, a Novel Phage with Potential Biocontrol Agent against Multidrug Resistant Escherichia coli

2017
Front Microbiol
PMCID: 5519627
PMID: 28785246
DOI: 10.3389/fmicb.2017.01355

[…] ila Genome Project (http://www.fruitfly.org/seq_tools/promoter.html), considering only sites located in intergenic regions (Reese, ) and Rho-independent transcription terminators were predicted using FindTerm program (http://linux1.softberry.com/berry.phtml?topic=findterm&group=programs&subgroup=gfindb; energy threshold value: −11) and ARNold server (http://rna.igmors.u-psud.fr/toolbox/arnold/), r […]

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FindTerm institution(s)
Department of Molecular Genetics and Biotechnology, The Hebrew University Hadassah Medical School, Jerusalem, Israel; Institute of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
FindTerm funding source(s)
Supported by the Human Frontier Science Program, the Swedish National Science Research Council, the Israeli Ministry of Science, Yeshaya Horowitz fellowship and THE ISRAEL SCIENCE FOUNDATION founded by The Academy of Sciences and Humanities - Centers of Excellence Program.

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