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). ...

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/. ...

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/ ...