DanQ – A Hybrid Convolutional and Recurrent Neural Network for predicting the function of DNA Sequences

DanQ

:: DESCRIPTION

DanQ is a hybrid convolutional and recurrent neural network model for predicting the function of DNA de novo from sequence.

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 DanQ

:: MORE INFORMATION

Citation

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences.
Quang D, Xie X.
Nucleic Acids Res. 2016 Apr 15. pii: gkw226.

SimConcept – Hybrid approach for simplifying Composite Named Entities in Biomedical Text

SimConcept

:: DESCRIPTION

SimConcept is a hybrid approach by integrating a machine learning model  with a pattern identification strategy to identify individual mentions from a composite named entity.

::DEVELOPER

SimConcept team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux / Windows
  • Perl

:: DOWNLOAD

 SimConcept

:: MORE INFORMATION

Citation

IEEE J Biomed Health Inform. 2015 Jul;19(4):1385-91. doi: 10.1109/JBHI.2015.2422651. Epub 2015 Apr 13.
SimConcept: a hybrid approach for simplifying composite named entities in biomedical text.
Wei CH, Leaman R, Lu Z.

Cerulean 0.1.1 – Hybrid Genome Assembler

Cerulean 0.1.1

:: DESCRIPTION

Cerulean is a hybrid assembly using high throughput short and long reads

::DEVELOPER

Son K. Pham

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 Cerulean

:: MORE INFORMATION

Citation

Viraj Deshpande, Eric DK Fung, Son Pham, Vineet Bafna,
Cerulean: A hybrid assembly using high throughput short and long reads (WABI2013)
rXiv preprint arXiv:1307.7933.

OLYMPUS – Hybrid Clustering method in Time Series Gene Expression

OLYMPUS

:: DESCRIPTION

OLYMPUS is an automated hybrid clustering method in the field of time series gene expression analysis.

::DEVELOPER

the Biosignal Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 OLYMPUS

:: MORE INFORMATION

Citation

OLYMPUS: an automated hybrid clustering method in time series gene expression. Case study: host response after Influenza A (H1N1) infection.
Dimitrakopoulou K, Vrahatis AG, Wilk E, Tsakalidis AK, Bezerianos A.
Comput Methods Programs Biomed. 2013 Sep;111(3):650-61. doi: 10.1016/j.cmpb.2013.05.025.

MR-MSPOLYGRAPH / MSPolygraph 1.61 – MapReduce Implementation of a Hybrid Spectral Library-Database Search Method for Large-scale Peptide Identification

MR-MSPOLYGRAPH / MSPolygraph 1.61

:: DESCRIPTION

MR-MSPOLYGRAPH is a MapReduce based implementation for parallelizing peptide identification from mass spectrometry data

MSPolygraph is an open source hybrid database and spectral library MS/MS search engine that runs in either serial or parallel modes. MSPolygraph examines the ions in MS/MS spectra to identify likely matching candidate peptides from a reference database of protein sequences (.Fasta file). MSPolygraph also supports searching a spectral library (collection of annotated MS/MS spectra).

::DEVELOPER

Ananth Kalyanaraman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 MR-MSPOLYGRAPH / MSPolygraph

:: MORE INFORMATION

Citation

A. Kalyanaraman, W.R. Cannon, B. Latt, D.J. Baxter (2011).
MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification.
Bioinformatics (2011) 27 (21): 3072-3073. doi: 10.1093/bioinformatics/btr523.

Cannon W.R., K.H. Jarman, B.M. Webb-Robertson, D.J. Baxter, C.S. Oehmen, K.D. Jarman, A. Heredia-Langner, G.A. Anderson, and K.J. Auberry. 2005.
Comparison of probability and likelihood models for peptide identification from tandem mass spectrometry data”,
J. Proteome Research, 4(5): 1687-169

RAPTR-SV 0.0.10 – Hybrid Method for Detection of Structural Variants

RAPTR-SV 0.0.10

:: DESCRIPTION

RAPTR-SV (ReAdPair spliT – Read Structural Variant) uses Read Pair and Split Read methods to identify structural variants in paired-end WGS data

::DEVELOPER

RAPTR-SV team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOSX
  • JDK for Java
  • MrsFAST

:: DOWNLOAD

 RAPTR-SV

:: MORE INFORMATION

Citation

RAPTR-SV: a hybrid method for the detection of structural variants.
Bickhart DM, Hutchison JL, Xu L, Schnabel RD, Taylor JF, Reecy JM, Schroeder S, Van Tassell CP, Sonstegard TS, Liu GE.
Bioinformatics. 2015 Feb 16. pii: btv086.

HRSS 0.2 – Hybrid Relative Specificity Similarity based on Gene Ontology

HRSS 0.2

:: DESCRIPTION

HRSS provides a hybrid GO-based semantic similarity algorithm for evaluating the functional similarity between GO terms or gene products.

:: DEVELOPER

Center for Plant Environmental Sensing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MySQL

:: DOWNLOAD

 HRSS

:: MORE INFORMATION

Citation

Wu, X., Pang, E., Lin, K. and Pei, Z.M. (2013)
Improving the Measurement of Semantic Similarity between Gene Ontology Terms and Gene Products: Insights from an Edge- and IC-Based Hybrid Method.
PLoS One 8(5), e66745. doi:10.1371/journal.pone.0066745

HyDA 1.3.1 / Squeezambler 2.0.3 – Hybrid De Novo Assembler

HyDA 1.3.1 / Squeezambler 2.0.3

:: DESCRIPTION

HyDA is a multipurpose assembler, particularly tested for single cell and normal multicell genome co-assembly

Squeezambler is a divide-and-conquer algorithm for economical sequencing and assembly of all distinct genomes in a bacterial sample. The key idea here is exploiting sparsity, which is the small number of distinct genomes (~1000) in comparison to the huge number of cells (~100 trillion).

::DEVELOPER

Algorithmic Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HyDA / Squeezamler

:: MORE INFORMATION

Citation:

Narjes S. Movahedi, Elmirasadat Forouzmand, Hamidreza Chitsaz,
De Novo Co-assembly of Bacterial Genomes from Multiple Single Cells,
IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp 561-565, 2012

Bioinformatics. 2013 Aug 13. [Epub ahead of print]
Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities.
Taghavi Z, Movahedi NS, Draghici S, Chitsaz H.

HyDRA – Hybrid Distance-Score Rank Aggregation software for Gene Prioritization

HyDRA

:: DESCRIPTION

HyDRA is a new approach to genomic data aggregation which combines the advantages of score-based and combinatorial aggregation techniques.

::DEVELOPER

Minji Kim

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • MatLab

:: DOWNLOAD

 HyDRA

:: MORE INFORMATION

Citation

HyDRA: Gene Prioritization via Hybrid Distance-Score Rank Aggregation.
Kim M, Farnoud F, Milenkovic O.
Bioinformatics. 2014 Nov 18. pii: btu766.

HRM – Hybrid Regulatory Models

HRM

:: DESCRIPTION

HRM is a general statistical inference framework for stochastic transcription-translation networks.

::DEVELOPER

Andrea Ocone ,Guido Sanguinetti

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • MatLab

:: DOWNLOAD

 HRM

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Apr 1;29(7):910-6. doi: 10.1093/bioinformatics/btt069. Epub 2013 Feb 13.
Hybrid regulatory models: a statistically tractable approach to model regulatory network dynamics.
Ocone A1, Millar AJ, Sanguinetti G.