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The programs usage in Scientific publications FindTerm
BestPal
FoldRNA
FindMiRNA

FindTerm

Current microbiology
2016, 72(3), 235-241. DOI: 10.1007/s00284-015-0935-2

Isolation and Comparative Genomic Analysis of T1-Like Shigella Bacteriophage pSf-2

Jun, J. W. et al.,
1. College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 151-742, South Korea 2. Departments of Rheumatology, Bundang Jesaeng Hospital, Seongnam, 463-774, South Korea

... html) (mini- mum promoter score: 0.9). Rho-independent transcription terminators were identified using FindTerm programs (http://www.softberry.com) (energy threshold value: -11). Additional characteristics of the putative protein ...


Toxins
2016, 8(4), 113. doi:10.3390/toxins8040113

Identification and Characterization of the HicAB Toxin-Antitoxin System in the Opportunistic Pathogen Pseudomonas aeruginosa

Li, G. et al.,
Department of Microbiology, Third Military Medical University, Chongqing 400038, China

... The putative promoter and terminator were predicted by BPROM (http://linux1.softberry.com/berry. phtml) and FindTerm (http://www.softberry.com/berry.phtml?topic=findterm&group= programs&subgroup=gfindb), respectively. 4.3. DNA Extraction, RNA Purification and RT-PCR. ...


Frontiers in microbiology
2016, 7: 545. doi: 10.3389/fmicb.2016.00545

Genomics of three new bacteriophages useful in the biocontrol of Salmonella

Bardina, C. et al.,
Departament de Genetica i de Microbiologia, Molecular Microbiology, Universitat Autonoma de Barcelona, Barcelona, Spain

... Potential promoter regions and transcription terminators were predicted using the Softberry programs BProm (http://linux1.softberry.com/berry.phtml), FindTerm (Solovyev and Salamov, 2011), and TransTerm (Ermolaeva et al., 2000). ...


Genetics and molecular research: GMR
2015, 14(1), 190. DOI http://dx.doi.org/10.4238/2015.January.16.2

Bioinformatic analysis of phage AB3, a phiKMV-like virus infecting Acinetobacter baumannii

Zhang, J., Liu, X., Li, X. J.
1Department of Geriatrics Medicine, The Third People’s Hospital of Chongqing, Chongqing, China 2Department of General Internal Medicine, The First Brand, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China

... Transcription terminators in the phage AB3 genome were predicted using the FindTerm program available from Softberry and promoters in the phage AB3 genome were predicted using the BPROM program on the Softberry website (linux1. softberry.com/berry.phtml). ...


Virus genes
2015, 50(1), 118-128. DOI: 10.1007/s11262-014-1138-9

Complete nucleotide sequence of Klebsiella phage P13 and prediction of an EPS depolymerase gene

Shang et al.,
1. College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao, 266003, Shandong, China 2. Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China

... gov/genomes/MICROBES/glimmer_3.cgi) [ 11 , 12 ], and Softberry (http://?linux1.?softberry.? com). ... The rho-independent terminators were identified using FindTerm and the promoters were identified using Softberry (http://?linux1.?softberry.?com). ...


Archives of virology
2015, 160(2), 561-564. DOI: 10.1007/s00705-014-2221-1

Genomic structure of the Aeromonas bacteriophage pAh6-C and its comparative genomic analysis

Jun, J. et al.,
1. Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Former American Base of Gournes, Heraklion, 71003, Crete, Greece 2. Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 151-742, Republic of Korea

... html) (minimum promoter score: 0.9). Rho-independent transcription terminators were identified using the FindTerm program (http://?www.?softberry.?com) (energy threshold value: -11). Additional characteristics of the putative ...


Microbiology
2014, 160(Pt 2), 287-295. DOI:10.1099/mic.0.073783-0

Expression of the six chromate ion transporter homologues of Burkholderia xenovorans LB400

Acosta-Navarrete Y. M. et al.,
1 Instituto de Investigaciones Quimico-Biologicas, Universidad Michoacana, Morelia, Michoacan, Mexico 2 Laboratorio Estatal de Salud Publica, Secretaria de Salud de Michoacan, Morelia, Michoacan, Mexico

... software (http://molbiol-tools.ca/promscan/). Rho-independent bacterial terminators were searched using the program FindTerm (Softberry). Bacterial growth and susceptibility tests. Bacteria were grown routinely by diluting 1 ...


Journal of virology
2014, 88(5), 2461-2480. DOI:10.1128/JVI.03363-13

Cluster M mycobacteriophages Bongo, PegLeg, and Rey with unusually large repertoires of tRNA isotypes

Pope W. H. et al.,
a Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA b Department of Biology, Gonzaga University, Spokane, Washington, USA

... programs. Dot plots were constructed using the Gepard program (27), and further bioinformatic analyses were performed using the DNA Master, FindTerm (Softberry), Splitstree (28), GLAM2, GLAM2SCAN, and MEME (29) programs. ...


Microbiology
April 2013 vol. 159 no. Pt 4 665-677 DOI:10.1099/mic.0.063396-0

The regulatory mechanism of 2,4,6-trichlorophenol catabolic operon expression by HadR in Ralstonia pickettii DTP0602

Torii et al.,
1Department of System Science, Graduate School of Engineering, Okayama University of Science, 1-1 Ridaicho, Kita-ku, Okayama 700-0005, Japan 2Department of Biomedical Engineering, Faculty of Engineering, Okayama University of Science, 1-1 Ridaicho, Kita-ku, Okayama 700-0005, Japan

... The rho-independent terminator was predicted with FindTerm (Softberry; http://linux1. softberry.com/berry.phtml). ... The presence of rho-independent terminator in the R1 and R10 regions was sought using FindTerm (Softberry), but not located. ...


Annals of Microbiology
August 2013 DOI:10.1007/s13213-013-0717-7

Characterization of the cryptic plasmid pWCZ from Lactobacillus paracasei WCZ isolated from silage

Yezhi Fu, Zhengyuan Zhai, Haoran An, Yanling Hao
1. Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qing Hua East Road, Hai Dian District, Beijing, 100083, China

... DNASTAR software package was employed to detect direct and inverted repeats. Putative promoter and terminator predictions were analyzed with BPROM and FindTerm, respectively (http://linux1.softberry.com/berry.phtml). ...


Antonie van Leeuwenhoek
Volume 104, Issue 6 , pp 941-948 DOI:10.1007/s10482-013-0013-3

An Lrp-type transcriptional regulator controls expression of the Bacillus subtilis chromate transporter

Aguilar-Barajas et al.,
1. Instituto de Investigaciones Quimico-Biologicas, Universidad Michoacana, Edificio B-3, Ciudad Universitaria, 58030, Morelia, Mich., Mexico 3. Genomica Alimentaria, Universidad de la Cienega, Sahuayo, Mich., Mexico 2. Depto. Bioquimica, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico, D.F., Mexico

... bin/seq_tools/promoter.pl). Rho-independent bacterial terminators were searched using the program FindTerm (Softberry Inc., New York, NY, USA). Cloning of the ywrC-chr3N-chr3C gene cluster. The ywrC-chr3N-chr3C gene ...


Microbiology
November 2013 mic.0.073783-0 DOI:10.1099/mic.0.073783-0

Expression of the Six CHR Chromate Ion Transporter Homologues of Burkholderia xenovorans LB400

Acosta-Navarrete et al.,
1 Universidad Michoacana; 2 Laboratorio Estatal de Salud Publica

... Putative promoter sequences were identified employing PromScan software 109 (http://molbiol-tools.ca/promscan/). Rho-independent bacterial terminators were 110 searched using the program FindTerm (Softberry Inc.). 111 112 Bacterial growth and susceptibility tests ...


Microbiology
April 2013 vol. 159 no. Pt 4 691-700 DOI:10.1099/mic.0.064741-0

A Q-like transcription factor regulates biofilm development in Escherichia coli by controlling expression of the DLP12 lysis cassette

Karl-Gustav Rueggeberg 1, Faustino A. Toba 1, Mitchell G. Thompson 1, Bryan R. Campbell 1 and Anthony G. Hay 1,2
1Department of Microbiology, Cornell University, Ithaca, NY 14853, USA 2Institute for Comparative and Environmental Toxicology, Cornell University, Ithaca, NY 14853, USA

... Antiterminator predictions. essDp sequence encompassing 400 bp upstream of the translation start site was analysed for the presence of putative Rho-independent transcriptional terminators using FindTerm software from Softberry (Hagen et al., 2010). ...


Research in Microbiology
Volume 164, Issue 10, December 2013, Pages 979–986 DOI:10.1016/j.resmic.2013.08.007

Characterization and complete genome sequence of the Shigella bacteriophage pSf-1

Jun et al.,
a Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 151-742, Republic of Korea b Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea

... promoter.html) (minimum promoter score: 0.9). Rho-independent transcription terminators were identified using FindTerm programs (http://www.softberry.ru) (energy threshold value: ?11). Additional characteristics of the putative ...


Microbiology
May 2013 mic.0.063776-0 DOI:10.1099/mic.0.063776-0

Isolation, characterization and complete genome sequence of PhaxI: a phage of Escherichia coli O157:H7

Shahrbabak et al.,
1 Tehran University of Medical Sciences; 2 University of Helsinki; 3 Laval University

... 2004; Schattner et al., 2005). To find Rho-independent terminators, TransTerm 230 (Ermolaeva et al., 2000) and FindTerm (SoftBerry) were used. PHIRE was also used 231 to find phage regulatory elements (Lavigne et al., 2004). The genomic map was 232 ...


Current Microbiology
Volume 66, Issue 6 , pp 535-543 DOI:10.1007/s00284-013-0308-7

Characterization and Genome Sequencing of Phage Abp1, a New phiKMV-Like Virus Infecting Multidrug-Resistant Acinetobacter baumannii

Huang et al.,
1. Department of Microbiology, Third Military Medical University, Chongqing, 400038, China 2. Institute of Burn Research, Southwest Hospital, Third Military Medical University, Chongqing, China

... Bacte- riophage-specific promoters were determined using Neural Network Promoter Prediction [29] and PHIRE [30]. Tran- scriptional termination sites were determined using the FindTerm program (http://www.softberry.ru/berry.phtml). ...


PloS one
(2013). 8(5), e62933. DOI:10.1371/journal.pone.0062933

Genomic and Proteomic Analyses of the Terminally Redundant Genome of the Pseudomonas aeruginosa Phage PaP1: Establishment of Genus PaP1-Like Phages

Lu et al.,
Department of Microbiology, College of Basic Medical Science, Third Military Medical University, Chongqing, China

...Predicted promoter regions were identified using neural network promoter prediction [51], and putative terminator structures were identified using the web tool FindTerm (http://linux1.softberry.com/berry.phtml)....


BMC genomics
(2013). 14(1), 849. DOI:10.1186/1471-2164-14-849

The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum

Venkataramanan et al.,
1 Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA 2 Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA

...Rho independent terminators were predicted using RNAmotif [90], Erpin [91] and Findterm (http://www.softberry.com webcite). ...


World Journal of Microbiology and Biotechnology
Volume 28, Issue 3 , pp 865-869 DOI 10.1007/s11274-011-0883-3

The ChrA homologue from a sulfur-regulated gene cluster in cyanobacterial plasmid pANL confers chromate resistance

Esther Aguilar-Barajas (1) (2) Paulina Jeronimo-Rodriguez (1) Martha I. Ramirez-Diaz (1) Christopher Rensing (2) Carlos Cervantes (1)
1. Instituto de Investigaciones Quimico-Biologicas, Universidad Michoacana, Edificio B-3, Ciudad Universitaria, 58030, Morelia, Michoacan, Mexico 2. Department of Soil, Water, and Environmental Science, University of Arizona, Tucson, AZ, USA

... Promoter sequences were searched with the Neural Network Promoter Predic- tion (http://www.fruitfly.org/cgi-bin/seq_tools/promoter.pl software. Rho-independent terminators were predicted with the FindTerm (Softberry Inc.) program. ...


Archives of Virology
Volume 157, Issue 2 , pp 391-395 DOI 10.1007/s00705-011-1175-9

Complete genomic sequence of a T4-like bacteriophage, phiAS4, infecting Aeromonas salmonicida subsp. salmonicida

J. H. Kim et al.,
1. Laboratory of Aquatic Animal Medicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 151-742, Korea 2. Basic Science Institute for Cell Damage Control, Sogang University, Seoul, 121-742, Korea

... 13]. Rho-independent transcription terminators were also pre- dicted using the FindTerm program (http://www.softberry.ru/ berry.phtml?topic=findterm&group= programs&subgroup= gfindb) (energy threshold value: -11). Additional ...


BMC Microbiology
2012, 12:10 doi:10.1186/1471-2180-12-10

Characterisation of the mgo operon in Pseudomonas syringae pv. syringae UMAF0158 that is required for mangotoxin production

Eva Arrebola 1* et al.,
1 Instituto de Hortofruticultura Subtropical y Mediterranea "La Mayora" (IHSM-UMA-CSIC), Estacion Experimental La Mayora, Algarrobo-Costa, 29750 Malaga, Spain 2 Instituto de Hortofruticultura Subtropical y Mediterranea "La Mayora" (IHSM-UMA-CSIC). Departamento de Microbiologia, Facultad de Ciencias, Universidad de Malaga, Unidad Asociada al CSIC, Campus de Teatinos, 29071 Malaga, Spain

... The promoter prediction software BPROM (SoftBerry Inc.) was used to identify possible promoters in the putative mgo operon. ... The entire sequence of 118 bp was also analysed by FindTerm software (SoftBerry Inc.) to locate putative Rho-independent bacterial terminators. ...


Front Microbiol.
2012; 3: 2. doi: 10.3389/fmicb.2012.00002

IncP-1e Plasmids are Important Vectors of Antibiotic Resistance Genes in Agricultural Systems: Diversification Driven by Class 1 Integron Gene Cassettes

Holger Heuer et al.,
1Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Julius Kuhn-Institut, Braunschweig, Germany 2Department de Ciencias Biologicas, Universidad Adolfo Ibanez, Santiago, Chile

... to GenBank sequences. Additional searches for genes, operons, promoters, and terminators were done using FGENESB, BPROM, and FindTerm at www.softberry. com (Softberry, Mount Kisco, NY, USA). The sequence data ...


PLoS ONE
7(5): e38283. (2012) doi:10.1371/journal.pone.0038283

Molecular Characterization of Podoviral Bacteriophages Virulent for Clostridium perfringens and Their Comparison with Members of the Picovirinae.

Volozhantsev NV et al.,
1 State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, Russian Federation, 2 Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, Athens, Georgia, United States of America,

...Protein-encoding genes (ORFs) were predicted using GeneMark.hmm for prokaryotes version 2.4 (http://opal.biology.gatech.edu/GeneMark) [73] and SoftBerry FGENESB (http://linux1.softberry.com/berry.phtml; Mount Kisco, NY, USA) programs. ... Putative promoters were analyzed by using Martin Reese's neural network prediction program at http://www.fruitfly.org/seq_tools/promot?er.html and BPROM (Softberry, Inc., Mount Kisco, NY, USA) at its website http://linux1.softberry.com/berry.phtml. Potential transcriptional terminators were assessed using the software programs TransTerm at the Nano+Bio-Center (http://nbc3.biologie.uni-kl.de) and FindTerm (Softberry, Inc., Mount Kisco, NY, USA) at the web site http://linux1.softberry.com/berry.phtml. ...


Plasmid
Volume 66, Issue 1, October 2011, Pages 7–18 DOI: 10.1016/j.plasmid.2011.03.002

Nucleotide sequence of Pseudomonas aeruginosa conjugative plasmid pUM505 containing virulence and heavy-metal resistance genes

M.I. Ramirez-Diaz a, , 1, , A. Diaz-Magana a, V. Meza-Carmen b, L. Johnstone c, C. Cervantes a, C. Rensing d
a Instituto de Investigaciones Quimico-Biologicas, Universidad Michoacana, Morelia, Michoacan, Mexico b Facultad de Ciencias Medicas y Biologicas “Dr. Ignacio Chavez”, Universidad Michoacana, Morelia, Michoacan, Mexico

... Rho-independent bacterial terminators were searched using the program FindTerm (Softberry Inc.). ... Search for genomic islands was made using CpG finger program from Softberry programs (http://www.linux1.softberry.com/berry.phtml). ...


RNA Biology
Volume 8, Issue 1 January/February 2011 Pages 11 - 13 DOI: 10.4161/rna.8.1.13346

ARNold: A web tool for the prediction of Rho-independent transcription terminators

Magali Naville, Adrien Ghuillot-Gaudeffroy, Antonin Marchais and Daniel Gautheret
Univ. Paris-Sud, Institut de Genetique et Microbiologie, Orsay Cedex, France

... search to intergenic regions, which makes it unfit for certain applications, including detection of transcriptional attenuators that occur after gene starts. Other available tools include com- mercial programs such as Softberry's Findterm (www.softberry. ...


Virology Journal
2011, 8:142 http://www.virologyj.com/content/8/1/142

Complete genome sequence of the lytic Pseudomonas fluorescens phage fjIBB-PF7A

Sillankorva et al.,
IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal

... proteins were determined using the ExPASy Compute pI/Mw tool http://au.expasy.org/ tools/pi_tool.html. Promoter predictions were made using promoter predictor http://www.fruitfly. org/seq_- tools/promoter.html, PHIRE 1.0 [28] and BPROM http:// linux1.softberry.com/berry.phtml ... ...Terminators were predicted using FindTerm http://linux1.softberry. com/berry.phtml?topic=findterm&group=programs&subgroup=gfindb ...


Veterinary Microbiology
Volume 153, Issues 3–4, 15 December 2011, Pages 403–406 DOI: 10.1016/j.vetmic.2011.05.050

The cps locus of Streptococcus suis serotype 16: Development of a serotype-specific PCR assay

Kaicheng Wang a, b, c, Weixing Fan c, Henk Wisselink d, Chengping Lu a, b
a Key Lab Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China b College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China

... Vector NTI. Putative promoter and terminator sequences were predicted by BPROM and FindTerm program on http://www.softberry.ru/berry.phtml, respectively. 2.4. Screening of serotype-specific gene. Cross-hybridization experiments ...


FEMS Microbiology Letters
(2011), 324: 117–124. doi: 10.1111/j.1574-6968.2011.02394.x

Genetic analysis of the capsular polysaccharide synthesis locus in 15 Streptococcus suis serotypes.

Wang, K., Fan, W., Cai, L., Huang, B. and Lu, C.
1Key Lab Animal Disease Diagnostic & Immunology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, China 2College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China

... Sequence annotation and bioinformatic analysis. The promoters and terminators of the sequenced cps locus were predicted using the bprom and findterm program (http://linux1.softberry.com/berry. phtml), respectively. ORFs were analyzed using the vectornt? program. ...


International Journal of Food Microbiology
Volume 151, Issue 2, 2 December 2011, Pages 171–181 DOI: 10.1016/j.ijfoodmicro.2011.08.019

Characterization of Streptococcus thermophilus two-component systems: In silico analysis, functional analysis and expression of response regulator genes in pure or mixed culture with its yogurt partner, Lactobacillus delbrueckii subsp. bulgaricus

Thevenard et al.,
a INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France b AgroParisTech, UMR1319 Micalis, F-78350 Jouy-en-Josas, France

... Presence of putative promoters, terminators and operons was evaluated using BPROM (http://linux1.softberry.com/berry.phtml) and BDGP (http://www.fruitfly.org/seq_tools/promoter. html), FINDTERM (http://linux1.softberry.com/berry.phtml), TransTermHP (http://transterm.cbcb ...


BMC Genomics
2011, 12:198 doi:10.1186/1471-2164-12-198

Characterization and genome sequencing of two Propionibacterium acnes phages displaying pseudolysogeny

Rolf Lood* and Mattias Collin
Department of Clinical Sciences, Division of Infection Medicine, BMC-B14, Lund University, SE-221 84 Lund, Sweden

... The genome of PAD20, PAS50 and PA6 were screened for putative sigma70- promoters using SAK and BPROM (Softberry, Inc.). ... Terminator structures were identified using FindTerm (Softberry, Inc.) and EMBOSS Explorer [43]. ...


Nucl. Acids Res.
(2011) 39 (13): 5622-5632. doi: 10.1093/nar/gkr166

Antisense RNA associated with biological regulation of a restriction–modification system

Iwona Mruk 1,2, Yaoping Liu 2,3, Liying Ge 2 and Ichizo Kobayashi 2,3,4
1Department of Microbiology, University of Gdansk, Kladki 24, Gdansk, 80-822, Poland, 2Department of Medical Genome Sciences, Graduate School of Frontier Sciences

... to agar plates. Bioinformatic analyses. In silico promoter prediction and terminator prediction were performed using the BPROM and FindTerm software, respectively (http://www.softberry.com/all.htm). RNA secondary structure ...


Bioscience, Biotechnology, and Biochemistry
Vol. 75 (2011) No. 5 P 944-952 DOI: 10.1271/bbb.100921

The Genome of Bacillus subtilis Phage SP10: A Comparative Analysis with Phage SPO1

YEE et al.,
1) Area of Biochemistry and Molecular Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University 2) Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture 3) Department of Bioscience, Tokyo University of Agriculture

... 2. The promoters recognized by the RNA polymerase holoenzyme containing sigma-A and the & independent terminators were predicted using the BPROM and the FindTerm program respectively (http://www.softberry.ru/ berry.phtml). They are shown in Fig. ...


J. Bacteriol.
August 2011 vol. 193 no. 15 3988-3997 doi: 10.1128/JB.05186-11

A Sulfite Respiration Pathway from Thermus thermophilus and the Key Role of Newly Identified Cytochrome c550

Robin et al.,
1Chemical and Environmental Science Department, Materials and Surface Science Institute, University of Limerick, Limerick, Ireland 2Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche c/o Dipartimento di Scienze Biochimiche, Sapienza Universita di Roma Piazzale Aldo Moro 5, I-00185 Rome, Italy

... are yet to be elucidated. A unique promoter upstream of TTHA1325 and a unique terminator region downstream of TTHA1327 were identified using BPROM and FindTerm (Softberry), respectively. Those findings showed that ...


PNAS
September 13, 2011 vol. 108 no. 37 E709-E717 doi: 10.1073/pnas.1101655108

Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia-specific small, noncoding RNAs required for virulence

Jovanka T. Koo a, Trevis M. Alleyne b,1, Chelsea A. Schiano a, Nadereh Jafari b, and Wyndham W. Lathem a,2
aDepartment of Microbiology-Immunology and bCenter for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611

...Predicted sRNAs were inspected for the presence of promoters and ?-independent terminators using the BProm and TermFind/RNAFold programs (Softberry)....


Journal of Bacteriology
May 2010, p. 2583-2595, Vol. 192, No. 10 doi:10.1128/JB.01526-09

The Actinomycin Biosynthetic Gene Cluster of Streptomyces chrysomallus: a Genetic Hall of Mirrors for Synthesis of a Molecule with Mirror Symmetry

Ullrich Keller,* Manuel Lang, Ivana Crnovcic, Frank Pfennig,§ and Florian Schauwecker
Institut fur Chemie, Arbeitsgruppe Biochemie und Molekulare Biologie, Technische Universitat Berlin, Franklinstrasse 29, D-10587 Berlin-Charlottenburg, Germany

.. Open reading frames (ORFs), operons, transcriptional start points, promoters, and terminators were identified using various computer programs such as FGENES-B (Softberry Inc.), SAK (21), BPROM (Softberry Inc.), and FindTerm (Softberry Inc.). ...


Plasmid
Volume 63, Issue 2, March 2010, Pages 108-117

Sequence analysis of plasmid pIR52-1 from Lactobacillus helveticus R0052 and investigation of its origin of replication

Hagen et al.,
a Department of Research and Development, Institut Rosell Inc., 6100 Avenue Royalmount, Montreal, Que., Canada H4P 2R2 b Department of Biology, Utah State University, Logan, UT 84322-5305, USA

... To predict the presence of rho-independent terminators, the Softberry FindTerm program (version 2.8) was used (http://www.softberry.ru/berry.phtml?group=programs&subgroup= gfindb&topic=findterm). 2.7. Analysis of repA genes for repeat sequences. ... 


Journal of Bacteriology
October 2010, p. 5441-5453, Vol. 192, No. 20 doi:10.1128/JB.00709-10

Brochothrix thermosphacta Bacteriophages Feature Heterogeneous and Highly Mosaic Genomes and Utilize Unique Prophage Insertion Sites

Samuel Kilcher, Martin J. Loessner, and Jochen Klumpp
Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland

... Rho-independent bacterial transcription terminators were predicted by using Softberry FindTerm (http://www.softberry.ru/berry.phtml?topic=findterm&group=programs&subgroup= gfindb) using an energy threshold value of –11 (default setting). ... 


Applied and Environmental Microbiology
October 2010, p. 6329-6337, Vol. 76, No. 19, doi:10.1128/AEM.01217-10

Functional Characterization of pGKT2, a 182-Kilobase Plasmid Containing the xplAB Genes, Which Are Involved in the Degradation of Hexahydro-1,3,5-Trinitro-1,3,5-Triazine by Gordonia sp. Strain KTR9

Indest et al.,
U.S. Army Engineer Research and Development Center, Environmental Laboratory, Vicksburg, Mississippi,1 Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada2

... 232 233 Open reading frames (ORFs) were identified using FGENESB program (Softberry Inc., 234 ... pGKT2 were analyzed for bacterial promoter elements and Rho independent terminator 236 sequences using BPROM and FindTerm programs (Softberry Inc.). ... 


Genomics
Volume 96, Issue 3, September 2010, Pages 167-172 doi:10.1016/j.ygeno.2010.06.001

Identification of lytic bacteriophage MmP1, assigned to a new member of T7-like phages infecting Morganella morganii

Zhu et al.,
Department of Microbiology, College of Basic Medical Science, Third Military Medical University, Chongqing 400038, China

... Bacteriophage-specific promoters were determined using Neural Network Promoter Prediction [32] and PHIRE [33]. Transcrptional termination sites were determined using FindTerm programs (http://www.softberry.ru/berry.phtml). ...


Microbiology
156 (2010), 2305-2315; DOI 10.1099/mic.0.038760-0

Detection and quantification of intergenic transcription in Mycoplasma hyopneumoniae

Stuart W. Gardner 1,2 and F. Chris Minion 1
1 Department of Veterinary Microbiology and Preventive Medicine, Interdepartmental Microbiology Program, Iowa State University, Ames, IA 50011, USA 2 Department of Statistics, Iowa State University, Ames, IA 50011, USA

... To identify stem–loop structures in the ig-072, ig-106, ig-282, ig-682 and ig-684 IG regions, SoftBerry FindTerm software was used. Heat-shock experimental design and data analysis. ... putative stem–loop structure as predicted by SoftBerry FindTerm software. ... 


BMC Microbiology
2010, 10:301doi:10.1186/1471-2180-10-301

Characterization of JG024, a pseudomonas aeruginosa PB1-like broad host range phage under simulated infection conditions

Garbe et al.,
1 Institute of Microbiology, Technische Universitat Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany 2 DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124 Braunschweig, Germany

... Two promoter regions were identified in this way. Rho-independent terminator structures were identified using the TransTerm [46] and FindTerm (Softberry, Inc.) software tools. The program MEME was used for identification of conserved intergenic motifs in phage JG024 [47]. ...


Carbohydrate Research
Volume 345, Issue 10, 2 July 2010, Pages 1422-1431 doi:10.1016/j.carres.2010.04.010

Cell surface display of chimeric glycoproteins via the S-layer of Paenibacillus alvei

Zarschler et al.,
Department fur NanoBiotechnologie, Vienna Institute of BioTechnology, Universitat fur Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria

... 50 Bacterial promoters, transcriptional terminators, operons and genes were 1 predicted by the BProm and FindTerm modules of the FGenesB gene prediction program in 2 Molquest software (SoftBerry, Mount Kisco, NY, USA). ...


Glycobiology
20 (6): 787-798. doi: 10.1093/glycob/cwq035

Protein tyrosine O-glycosylation—A rather unexplored prokaryotic glycosylation system

Zarschler et al.,
Department fur NanoBiotechnologie, Vienna Institute of BioTechnology, Universitat fur Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria

... 2000). Bacterial promoters, transcriptional terminators, operons and ORFs were predicted by the BProm and FindTerm modules of the FGenesB gene prediction program in Molquest software (SoftBerry Inc., Mount Kisco, NY). ...


BMC Microbiology
2010, 10:153 doi:10.1186/1471-2180-10-153

Transcriptome analysis of the mobile genome ICEclc in Pseudomonas knackmussii B13

Gaillard M, Pradervand N, Minoia M, Sentchilo V, Johnson DR, van der Meer JR.
1 Department of Fundamental Microbiology, University of Lausanne, Batiment Biophore, Quartier UNI-Sorge, 1015 Lausanne, Switzerland

... Bioinformatic tools. Putative promoters, terminators and transcription factor binding sites were predicted by using the BPROM and FindTerm programs on http://www.Softberry.com. The map of ICEclc was designed from SeqBuilder of the Lasergene software package ...


Food Microbiology
Volume 26, Issue 1, February 2009, Pages 52-57

Evidence of horizontal transfer as origin of strain to strain variation of the tyramine production trait in Lactobacillus brevis

Emmanuel Coton and Monika Coton
aADRIA Normandie, Boulevard du 13 juin 1944, 14310 Villers-Bocage, France

... Prokaryotic promoter prediction was performed using the Internet site http://www.fruitfly.org/ seq_tools/promoter.html; while, transcription terminators were predicted using the FindTerm program at http://www.softberry.ru. 3. Results and discussion. 3.1. ...


Nucleic Acids Research
2009 37(6):e46; doi:10.1093/nar/gkp080

Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing

Liu et al.,
1HHMI and Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, 2HHMI and Channing Laboratory, Boston, MA 02115 and 3Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA

... several sRNAs (IGR4, IGR6) were not identified in other bacteria by BLASTN analysis (Table 2). In addition, we analyzed the candidate sRNAs for nearby promoters and Rho-independent terminators using BPROM and FindTerm software available from Softberry (Mount Kisco ...


Research in Microbiology
Volume 160, Issue 6, July-August 2009, Pages 401-408

Characterization of salivaricin CRL 1328, a two-peptide bacteriocin produced by Lactobacillus salivarius CRL 1328 isolated from the human vagina

Esteban Vera Pingitore, Elvira Maria Hebert, Maria Elena Nader-Macias and Fernando Sesma
aCentro de Referencia para Lactobacilos (CERELA–CONICET), Chacabuco 145 (T4000ILC), San Miguel de Tucuman, Tucuman, Argentina

... The presence of putative promoter elements was predicted by Neural Network Promoter Prediction (http://www.fruitfly.org/seq_tools/promoter.html). Transcriptional terminators were predicted with the FindTerm algorithm (http://www.softberry.ru/berry.phtml). ...


Journal of Bacteriology
February 2009, p. 1056-1065, Vol. 191, No. 3

Transcription of clpP Is Enhanced by a Unique Tandem Repeat Sequence in Streptococcus mutans

Jiaqin Zhang 1,2, Anirban Banerjee 1, and Indranil Biswas 1*
Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, Kansas 66160,1 Department of Parasitology, Shandong University School of Medicine, 44# Wenhua Xi Road, Jinan, Shandong 250012, China2

... 55). The intergenic region between clpP and SMU.1671, which is 115 bp long, encodes a putative -independent terminator located between bp 85 and 109 that was identified by the FindTerm program (Softberry, Inc.). Figure ...


Journal of Bacteriology
May 2008, p. 3646-3657, Vol. 190, No. 10

Regulation of Gene Expression in a Mixed-Genus Community: Stabilized Arginine Biosynthesis in Streptococcus gordonii by Coaggregation with Actinomyces naeslundii

Nicholas S. Jakubovics,1 Steven R. Gill,2,4 Stacey E. Iobst,4 M. M. Vickerman,2,3 and Paul E. Kolenbrander
National Institute of Dental and Craniofacial Research, National Institutes of Health, Building 30, Room 310, Bethesda, Maryland 20892,1 Department of Oral Biology,2 Department of Periodontics and Endodontics, University at Buffalo School of Dentistry, Buffalo, New York,3 Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 208504

... gordonii genome sequence were detected using the BProm and FindTerm modules of the fgenesB gene prediction program in Molquest software (Softberry Inc., Mount ...


Journal of Bacteriology
doi:10.1128/JB.01436-08 JB Accepts, published online ahead of print on 1 December 2008

Transcription of clpP is enhanced by a unique tandem repeat sequence in Streptococcus mutans

Jiaqin Zhang, Anirban Banerjee, and Indranil Biswas
Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160; Department of Parasitology, Shandong University School of Medicine, 44# Wenhua Xi Road, Jinan, Shandong, 250012, P R China

... encodes a putative ?-independent terminator located between 85- and 109-bp that was identified 18 by FindTerm program (Softberry Inc.). 19 ...


Food Microbiology
doi:10.1016/j.fm.2008.07.009

Evidence of horizontal transfer as origin of strain to strain variation of the tyramine production trait in Lactobacillus brevis

Emmanuel Coton and Monika Coton
ADRIA Normandie, Boulevard du 13 juin 1944, 14310 Villers-Bocage, France

... site http://www.fruitfly.org/seq_tools/promoter.html; while, transcription terminators were predicted using the FindTerm program at http://www.softberry.ru. ...


Microbiology
154 (2008), 1422-1435; DOI 10.1099/mic.0.2007/014365-0

Genes for two multicopper proteins required for Fe(III) oxide reduction in Geobacter sulfurreducens have different expression patterns both in the subsurface and on energy-harvesting electrodes

Dawn E. Holmes et. al.,
Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA

... FGENESB, BPROM and FindTerm programs, available through SoftBerry (www.softberry. com), were used for operon and gene predictions. RESULTS. ...


Nucleic Acids Research
doi:10.1093/nar/gkm836 published online on October 16, 2007

Characterization of bacterial operons consisting of two tubulins and a kinesin-like gene by the novel Two-Step Gene Walking method

Martin Pilhofer et al.,
Lehrstuhl fur Mikrobiologie, Technical University Munich, Am Hochanger 4, D-85354 Freising, Germany

... The prediction of Rho-independent terminators was performed with the program FindTerm (www.softberry.com/berry.phtml?topic=findterm&group=programs&subgroup ...


Microbiology
153 (2007), 2148-2158;

ss-Dependent carbon-starvation induction of pbpG (PBP 7) is required for the starvation-stress response in Salmonella enterica serovar Typhimurium

William J. Kenyon et al.,
Department of Biomedical Sciences, University of South Alabama, Mobile, AL 36688, USA

... Relevant nucleotide sequences were retrieved using the NCBI's Entrez server. Bacterial terminator analysis was done using FindTerm (http://www.softberry.com/). ...


Plasmid
Volume 57, Issue 1, January 2007, Pages 44-54

Complete nucleotide sequence of pBMB67, a 67-kb plasmid from Bacillus thuringiensis strain YBT-1520

Liu Chao et al.,
State Key Laboratory of Agricultural Microbiology and National Engineering Research Center of Microbe Pesticides, Huazhong Agricultural University, Wuhan 430070, China

... Promoter and terminator predictions were performed using BPROM and FindTerm, respectively (http://www.softberry.com/berry.phtml). ...


Enzyme and Microbial Technology
Volume 40, Issue 4, 5 March 2007, Pages 747-753

Genetic and biochemical characterization of an a-l-arabinofuranosidase isolated from a compost starter mixture

Kurt Wagschal et al.,
USDA Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, United States

... the sequences for bacterial promoters and rho-independent transcription termination sites was performed using BPROM and FindTerm, available at www.softberry.com ...


Journal of Bacteriology,
June 2006, p. 4362-4372, Vol. 188, No. 12

Characterization of a Novel Partition System Encoded by the d and w Genes from the Streptococcal Plasmid pSM19035

Micha Dmowski,* Izabela Sitkiewicz, and Piotr Cegowski
Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawiskiego 5A, 02-106 Warsaw, Poland

... Despite the presence of a putative rho-independent terminator (FindTerm; Softberry) (positions 6281 to 6337 in pBT233), we wanted to confirm that and ...


Molecular Microbiology,
Volume 59, Number 2, January 2006, pp. 541-550(10)

A small RNA inhibits translation of the histone-like protein Hc1 in Chlamydia trachomatis
Grieshaber, N.A.(1); Grieshaber, S.S.(1); Fischer, E.R.(2); Hackstadt, T.
1: Host-Parasite Interactions Section, Laboratory of Intracellular Parasites, and 2: Microscopy Core Facility, NIAID, NIH, Rocky Mountain Laboratories, Hamilton, MT 59840, USA.

... promoter sequences and rho-independent terminators that could result in an 120 bp product using the BPROM and FindTerm utilities (http://www.softberry.com). ...


Journal of Bacteriology,
January 2006, p. 160-168, Vol. 188, No. 1

Identification of the syr-syp Box in the Promoter Regions of Genes Dedicated to Syringomycin and Syringopeptin Production by Pseudomonas syringae pv. syringae B301D

Nian Wang,1, Shi-En Lu,1, Qingwu Yang,2 Sing-Hoi Sze,3 and Dennis C. Gross1*
Department of Plant Pathology and Microbiology,1 Department of Computer Science,2 Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 778433

... typical rho-independent terminators, located after the syrP-syrD-sypA-sypB operon and the syrC gene, were identified by the FindTerm program (Softberry) (Fig. ...


Journal of Bacteriology,
January 2006, p. 202-210, Vol. 188, No. 1

Reconstruction and Regulation of the Central Catabolic Pathway in the Thermophilic Propionate-Oxidizing Syntroph Pelotomaculum thermopropionicum

Tomoyuki Kosaka,1 Taku Uchiyama,1 Shun-ichi Ishii,1 Miho Enoki,1,2 Hiroyuki Imachi,3 Yoichi Kamagata,2 Akiyoshi Ohashi,3 Hideki Harada,3 Hiroshi Ikenaga,1 and Kazuya Watanabe1*
Laboratory of Applied Microbiology, Marine Biotechnology Institute, Kamaishi, Iwate 026-0001,1 Japan3

... were manually checked. Terminator sequences were analyzed using the FindTerm program (SoftBerry). Molecular weights and isoelectric ...


Molecular Microbiology,
Volume 59, Number 2, January 2006, pp. 541-550(10)

A small RNA inhibits translation of the histone-like protein Hc1 in Chlamydia trachomatis

Grieshaber, N.A.(1); Grieshaber, S.S.(1); Fischer, E.R.(2); Hackstadt, T.
1: Host-Parasite Interactions Section, Laboratory of Intracellular Parasites, and 2: Microscopy Core Facility, NIAID, NIH, Rocky Mountain Laboratories, Hamilton, MT 59840, USA.

... promoter sequences and rho-independent terminators that could result in an 120 bp product using the BPROM and FindTerm utilities (http://www.softberry.com). ...


BestPal

Genetica
Volume 131, Number 3 / November 2007 p. 255-265

Isolation, gene structure, and comparative analysis of the S-layer gene sslA of Sporosarcina ureae ATCC 13881

Pavel M. Ryzhkov, , Kai Ostermann and Gerhard Rodel
Institut fu"r Genetik, Technische Universita"t Dresden, Helmholtzstr. 10, 01062 Dresden, Germany

... sequences and promoter regions were identified by means of BestPal and Bprom programs from ''SoftBerry'' software package (http://www.softberry.com). ...


FoldRNA

PLoS ONE
7(5): e36709. doi:10.1371/journal.pone.0036709

The mbo Operon Is Specific and Essential for Biosynthesis of Mangotoxin in Pseudomonas syringae

Carrion VJ, Arrebola E, Cazorla FM, Murillo J, de Vicente A
Instituto de Hortofruticultura Subtropical y Mediterranea “La Mayora” (IHSM-UMA-CSIC), Departamento de Microbiologia, Facultad de Ciencias, Universidad de Malaga, Malaga, Spain Laboratorio de Patologia Vegetal, ETS de Ingenieros Agronomos, Universidad Publica de Navarra, Pamplona, Spain

...The promoter (BPROM) and terminator (FindTerm and FoldRNA) prediction was performed using SoftBerry online programmes (http://www.softberry.com, Mount Kisco, NY, USA). ...


PNAS
September 13, 2011 vol. 108 no. 37 E709-E717 doi: 10.1073/pnas.1101655108

Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia-specific small, noncoding RNAs required for virulence

Jovanka T. Koo a, Trevis M. Alleyne b,1, Chelsea A. Schiano a, Nadereh Jafari b, and Wyndham W. Lathem a,2
aDepartment of Microbiology-Immunology and bCenter for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611

...Predicted sRNAs were inspected for the presence of promoters and ?-independent terminators using the BProm and TermFind/RNAFold programs (Softberry)....


Nature Protocols
ISSN 1750-2799 2009 DOI: 10.1038/nprot.2009.15

Efficient in silico Designing of Oligonucleotides for Artificial Gene Synthesis.

Garg, Abhishek D.
Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom

... 1. DNA mfold v.3.2 URL: http://frontend.bioinfo.rpi.edu/applications/mfold/cgi-bin/dna-form1.cgi. 2. FoldRNA URL: http://www.softberry.com/berry.phtml?topic=foldrna&group=programs&subgroup= rnastruct. 3. Gene Design ?2.0 URL: http://baderlab.bme.jhu.edu/gd/. ...


FindMiRNA

Open Journal of Genetics
Vol.4 No.3(2014), Article ID:47053,12 pages DOI:10.4236/ojgen.2014.43020

Microsatellites and the Polyploid Guarana Plant: Diversity under a Sea of Alleles

da Silva Angelo P. C. et al.,
1Embrapa Western Amazon, Manaus, Brazil 2CNPq Fellowship at Embrapa Western Amazon, Manaus, Brazil

...On the other hand, the same TA repeat block displays a predicted potential to function as a TATA box (Softberry-TSSP) and to promote the transcription of smRNAs located downstream. ... ...Finally, there is at least one predicted pre-miRNA (Softberry-findmirna) in the MFT 3’-UTR, which could generate 21 or 24 nucleotides long mature miRNAs with the sequence 5’-ugccaggcguaauauauauau(aua)-3’ (Figure 4(b)). ...


PLoS ONE
(2013), 8(3): e56694. doi:10.1371/journal.pone.0056694

De novo Transcriptome Sequencing Reveals a Considerable Bias in the Incidence of Simple Sequence Repeats towards the Downstream of ‘Pre-miRNAs’ of Black Pepper.

Joy N, Asha S, Mallika V, Soniya EV
Plant Molecular Biology, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, Kerala, India

... From the identified transcripts bearing SSRs, the 'unannotated transcripts' which were considered as non-coding alone were chosen and subjected to miRNA predictions using 'findMiRNA' programme [35]of Softberry (www.softberry.com. Accessed 2013 Jan 17). ...


Functional & Integrative Genomics
Volume 12, Issue 2 , pp 387-395 DOI 10.1007/s10142-012-0267-2

Identification of an miRNA candidate reflects the possible significance of transcribed microsatellites in the hairpin precursors of black pepper

Nisha Joy (1) Eppurathu Vasudevan Soniya (1)
1. Plant Molecular Biology, Rajiv Gandhi Centre for Biotechnology, Thycaud P O, Poojappura, Thiruvananthapuram, 695 014, Kerala, India

... Hence, the sequence was analysed miRNA prediction tools like 'findMiRNA' programme (Adai et al. 2005) of Softberry (www.softberry. ... b The predicted position of pre- miRNA and mature miRNA using 'findMiRNA' of Softberry. ...


Journal of Bioinformatics and Sequence Analysis
Vol. 3(2), pp. 11-22, February 2011

Avian influenza and micro RNA: Role of bioinformatics

Pankaj Koparde 1 and Shailza Singh 2 *
1 Institute of Bioinformatics and Biotechnology, University of Pune, Pune -411007, India. 2National Centre for Cell Science, Pune University Campus, Pune -411007, India.

... Also, prediction of metazoan miRNAs for NS1 homologous proteins from humans was also carried out. This was done using Softberry findmiRNA, miReval, TargetScanS and DIANA microT web tools. ... Softberry findmiRNA http://www.softberry.com/ ...



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