Tag: optimization

GECKO – GEnetic Classification using k-mer Optimization

GECKO

:: DESCRIPTION

GECKO is a genetic algorithm toclassify and extract meaningful sequences from multiple types of sequencing approaches including mRNA, microRNA, and DNA methylome data.

::DEVELOPER

GECKO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

GECKO

:: MORE INFORMATION

Citation

Thomas A, Barriere S, Broseus L, Brooke J, Lorenzi C, Villemin JP, Beurier G, Sabatier R, Reynes C, Mancheron A, Ritchie W.
GECKO is a genetic algorithm to classify and explore high throughput sequencing data.
Commun Biol. 2019 Jun 20;2:222. doi: 10.1038/s42003-019-0456-9. PMID: 31240260; PMCID: PMC6586863.

MO-SAStrE v2.0 – Multiobjective Optimization for Sequence Alignments based on Structural Evaluations

MO-SAStrE v2.0

:: DESCRIPTION

MO-SAStrE proposes a multiobjective genetic approach that takes advantage of three different objectives: STRIKE score (based on structural information), totally conserved (TC) columns and percentage of non-gaps. Additionally, this algorithm also applies a novel codification of individuals as well as efficient mutation and crossover operators. This algorithm is implemented through the well-known multiobjective non-dominated sorting genetic algorithm (NSGA-II) approach.

::DEVELOPER

Francisco M. Ortuño Guzman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX /Windows
  • MatLab

:: DOWNLOAD

 MO-SAStrE

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 1;29(17):2112-21. doi: 10.1093/bioinformatics/btt360. Epub 2013 Jun 21.
Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns.
Ortuño FM1, Valenzuela O, Rojas F, Pomares H, Florido JP, Urquiza JM, Rojas I.

CICERO v1.8.1 – Clipped-reads Extended for RNA Optimization

CICERO v1.8.1

:: DESCRIPTION

CICERO is an assembly-based algorithm to detect diverse classes of driver gene fusions from RNA-seq.

::DEVELOPER

Zhang (Jinghui Zhang) Lab,St. Jude Children’s Research Hospital

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac

:: DOWNLOAD

CICERO

:: MORE INFORMATION

Citation

Tian L, Li Y, Edmonson MN, Zhou X, Newman S, McLeod C, Thrasher A, Liu Y, Tang B, Rusch MC, Easton J, Ma J, Davis E, Trull A, Michael JR, Szlachta K, Mullighan C, Baker SJ, Downing JR, Ellison DW, Zhang J.
CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
Genome Biol. 2020 May 28;21(1):126. doi: 10.1186/s13059-020-02043-x. PMID: 32466770; PMCID: PMC7325161.

RADinitio 1.1.1 – Simulation software for the Selection and Optimization of RADseq Experiments

RADinitio 1.1.1

:: DESCRIPTION

RADinitio is a forward simulator for creating population-level RAD data sets, based on a given reference genome. This in silico RADseq library preparation and sequencing process, allows for the exploration of parameters including restriction enzyme selection, library insert size, PCR duplicate distribution, and sequencing coverage.

DEVELOPER

Cresko labs

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

RADinitio

:: MORE INFORMATION

Citation:

Rivera-Colón AG, Rochette NC, Catchen JM.
Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data.
Mol Ecol Resour. 2021 Feb;21(2):363-378. doi: 10.1111/1755-0998.13163. Epub 2020 May 20. PMID: 32275349.

MOSAICS 4.0 / PymoSAICS 0.2.0 – Methodologies for Optimization and SAmpling In Computational Studies

MOSAICS 4.0 / PymoSAICS

:: DESCRIPTION

MOSAICS is a sampling program developed to improve sampling efficiency by incorporating natural move-sets for proteins and nucleic acids.

MOSAICS-EM is a software package designed to refine molecular conformations directly against two-dimensional (2D) electron-microscopy images.

PymoSAICS is a pyMol plugin of MOSAICS.

::DEVELOPER

MOSAICS team

:: SCREENSHOTS

PymoSAICS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Python
  • pyMOL

:: DOWNLOAD

 MOSAICS / PymoSAICS

:: MORE INFORMATION

Citation

Exploring peptide/MHC detachment processes using Hierarchical Natural Move Monte Carlo.
Knapp B, Demharter S, Deane CM, Minary P.
Bioinformatics. 2015 Sep 22. pii: btv502

GISMO 2.0 – Gibbs Sampler for Multi-alignment Optimization

GISMO 2.0

:: DESCRIPTION

GISMO is a Bayesian Markov chain Monte Carlo (MCMC) sampler for protein multiple sequence alignment (MSA)

::DEVELOPER

GISMO team

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GISMO

:: MORE INFORMATION

Citation

Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties.
Neuwald AF, Altschul SF.
PLoS Comput Biol. 2016 May 18;12(5):e1004936. doi: 10.1371/journal.pcbi.1004936.

CRISPR-DO 0.1 – Genome-wide CRISPR Design and Optimization

CRISPR-DO 0.1

:: DESCRIPTION

CRISPR-DO is a web application for the Design and Optimization of guide sequences in several genomes (human, mouse, fly, worm and zebrafish). CRISPR-DO integrates an sgRNA efficiency prediction model (Xu, et al., 2015) and an off-target scoring function (Hsu, et al., 2013), which allow the users to evaluate the “goodness” of an sgRNA in both sensitivity and specificity.

::DEVELOPER

CRISPR-DO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX
  • Python

:: DOWNLOAD

 CRISPR-DO

:: MORE INFORMATION

Citation:

CRISPR-DO for genome-wide CRISPR design and optimization.
Ma J, Köster J, Qin Q, Hu S, Li W, Chen C, Cao Q, Wang J, Mei S, Liu Q, Xu H, Liu XS.
Bioinformatics. 2016 Jul 10. pii: btw476.

EPISOFT – Epitope Vaccine Optimization Server

EPISOFT

:: DESCRIPTION

EPISOFT predicts epitope HLA I binding profiles and computes population protection (PPC). It also identifies minimal sets of epitopes that reach a target PPC for 5 distinct user-selected ethnic groups.

::DEVELOPER

Immunomedicine Group 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

Towards the Knowledge-based Design of Universal Influenza Epitope Ensemble Vaccines.
Sheikh QM, Gatherer D, Reche PA, Flower DR.
Bioinformatics. 2016 Jul 10. pii: btw399.

PhySamp 1.1.0 – Phylogenetic Sampling and Optimization of Sequence Alignments

PhySamp 1.1.0

:: DESCRIPTION

PhySamp is a package dedicated to phylogenetic sampling. It samples a sequence alignment according to its corresponding phylogenetic tree.

::DEVELOPER

Dr Julien Y. Dutheil

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

PhySamp

:: MORE INFORMATION

Citation

Dutheil JY1,2, Figuet E3.
Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off.
BMC Bioinformatics. 2015 Jun 9;16:190.

DOTcvpSB 2010_E4 – Matlab Toolbox for Dynamic Optimization in Systems Biology

DOTcvpSB 2010_E4

:: DESCRIPTION

DOTcvpSB is a software toolbox which uses the CVP approach for handling continuous and mixed integer DO problems. DOTcvpSB has been successfully applied to several problems in systems biology and bioprocess engineering. The toolbox is written in MATLAB and provides an easy to use environment while maintaining a quite good performance. DOTcvpSB is designed for the Windows operating systems. The toolbox also contains a function for importing SBML models.

::DEVELOPER

(Bio)Process Engineering group, IIM-CSIC

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Matlab

:: DOWNLOAD

 DOTcvpSB

:: MORE INFORMATION

Citation:

T. Hirmajer, E. Balsa-Canto and J. R. Banga:
DOTcvpSB, a software toolbox for dynamic optimization in systems biology.
BMC Bioinformatics 2009, 10:199

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