Tag: Designing

PRISE – Designing Sequence-selective PCR Primers

PRISE

:: DESCRIPTION

PRISE (PRImer Selector) is an interactive software package for PCR primer design. PRISE enables the design of sequence-specific / sequence-selective PCR primers. One important feature of PRISE is that it automates the task of placing primer-template mismatches at the 3′ end of the primers – a property that is crucial for sequence selectivity / specificity

::DEVELOPER

Rachid Ounit, Algorithms and Computational Biology Lab ,University of California

:: SCREENSHOTS

PRISE

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  PRISE

:: MORE INFORMATION

Citation

J Microbiol Methods. 2008 Mar;72(3):263-7. doi: 10.1016/j.mimet.2007.12.004.
PRISE (PRImer SElector): software for designing sequence-selective PCR primers.
Fu Q1, Ruegger P, Bent E, Chrobak M, Borneman J.

CancerIN – Classification and Designing of Anticancer Compounds

CancerIN

:: DESCRIPTION

CancerIN  is a web server developed for predicting anticancer activity of molecules. Similarity based approach has been used for discrimination or classification of anticancer and non-anticancer molecule.

::DEVELOPER

CancerIN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOs
  • Python

:: DOWNLOAD

CancerIN

:: MORE INFORMATION

Citation

Prediction of anticancer molecules using hybrid model developed on molecules screened against NCI-60 cancer cell lines.
Singh H, Kumar R, Singh S, Chaudhary K, Gautam A, Raghava GP.
BMC Cancer. 2016 Feb 9;16:77. doi: 10.1186/s12885-016-2082-y.

PrimerFactoryQt 1.0.3 beta- Tool for Searching and Designing Primers

PrimerFactoryQt 1.0.3 beta

:: DESCRIPTION

PrimerFactoryQt is a tool for searching and designing primers. The Primer Search is based on Bowtie, an ultrafast, memory-efficient alignment program for aligning short DNA sequence. You can build your specific oligo database and search it against your query sequence. Consequently you find out, where your available primers will bind. Laboriously quests or new ordering of oligos is not anymore required. In addition you can save the search hits as features in a genbank file format.

::DEVELOPER

Stefanie Lück

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

PrimerFactoryQt

:: MORE INFORMATION

ProtocolNavigator 1.0 – Open-source software for Designing, Documenting Biological Experiments

ProtocolNavigator 1.0

:: DESCRIPTION

ProtocolNavigator is a virtual laboratory environment that promote reproducibility of biological experiments and reuse of experimental data.

::DEVELOPER

ProtocolNavigator team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 ProtocolNavigator

:: MORE INFORMATION

Citation

ProtocolNavigator: emulation based software for the design, documentation and reproduction biological experiments.
Khan IA, Fraser A, Bray MA, Smith PJ, White NS, Carpenter AE, Errington RJ.
Bioinformatics. 2014 Aug 22. pii: btu554.

IL4pred – Designing and Disovering of Interleukin-4 inducing peptides

IL4pred

:: DESCRIPTION

IL4pred web server is developed for users working in the field of vaccine design. This server allows users to predict and design Interleukin-4 (IL4) inducing peptides.

::DEVELOPER

IL4pred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Prediction of IL4 inducing peptides.
Dhanda SK, Gupta S, Vir P, Raghava GP.
Clin Dev Immunol. 2013;2013:263952. doi: 10.1155/2013/263952.

VaccineDA – Designing Vaccine Adjuvants based on immunomodulatory DNA

VaccineDA

:: DESCRIPTION

VaccineDA is a webserver in order to assist the experimentalists in designing better IMODN based adjuvants using sequence information of the oligonucleotides. The models used in prediction have been developed on experimentally validated IMODNs using different Datasets.

::DEVELOPER

VaccineDA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

VaccineDA: Prediction, design and genome-wide screening of oligodeoxynucleotide-based vaccine adjuvants.
Nagpal G, Gupta S, Chaudhary K, Dhanda SK, Prakash S, Raghava GP.
Sci Rep. 2015 Jul 27;5:12478. doi: 10.1038/srep12478.

desiRm – Designing siRNA for Silencing a Gene

desiRm

:: DESCRIPTION

desiRm is a webserver for designing highly effective siRNA for silencing a gene. This tool will be helpful to design siRNA to degrade disease isoform of heterozygous single nucleotide polymorphism gene without depleting the wild type protein.

::DEVELOPER

desiRm team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2011;6(8):e23443. doi: 10.1371/journal.pone.0023443. Epub 2011 Aug 10.
Designing of highly effective complementary and mismatch siRNAs for silencing a gene.
Ahmed F1, Raghava GP.

AntiCP – Prediction and Designing of Anticancer Peptides

AntiCP

:: DESCRIPTION

AntiCP is web based prediction server for Anticancer peptides. SVM models developed are based on amino acid composition and binary profile features. Positive dataset consists of 225 antimicrobial peptides with anticancer properties.

::DEVELOPER

AntiCP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Sci Rep. 2013 Oct 18;3:2984. doi: 10.1038/srep02984.
In silico models for designing and discovering novel anticancer peptides.
Tyagi A1, Kapoor P, Kumar R, Chaudhary K, Gautam A, Raghava GP.

SPiM 0.05 / SPiM Player 1.13 – Programming Language for Designing and Simulating Computer Models of Biological Processes

SPiM 0.05 / SPiM Player 1.13

:: DESCRIPTION

The SPiM (Stochastic Pi Machine) is a programming language for designing and simulating computer models of biological processes. The language is based on a mathematical formalism known as the pi-calculus, and the simulation algorithm is based on standard kinetic theory of physical chemistry. The language features a simple graphical notation for modelling a range of biological systems, and can be used to model large systems incrementally, by directly composing simpler models of subsystems.

The SPiM Player is a graphical interface to SPiM

::DEVELOPER

Andrew Phillips, Luca Cardelli, Matthew Lakin, Filippo Polo, Microsoft Research.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SPiM / SPiM Player

:: MORE INFORMATION

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