Tag: de novo

BOSS – Predicting Biological System Objectives de novo from internal State Measurements

BOSS

:: DESCRIPTION

BOSS (Biological Objective Solution Search) is a novel method for the inference of an objective function of a biological system from its underlying network stoichiometry as well as experimentally-measured state variables.

::DEVELOPER

the Computational Systems Biology Laboratory, Department of Biomedical Engineering, University of Virginia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • GAMS

:: DOWNLOAD

 BOSS

:: MORE INFORMATION

Citation:

Gianchandani, E.P., M.A. Oberhardt, A.P. Burgard, C.D. Maranas, and J.A. Papin. 2008.
Predicting biological system objectives de novo from internal state measurements.
BMC Bioinformatics, 9:43

isONclust 0.0.4 – de novo Clustering of long Transcript Reads into Genes

isONclust 0.0.4

:: DESCRIPTION

isONclust is a tool for clustering either PacBio Iso-Seq reads, or Oxford Nanopore reads into clusters, where each cluster represents all reads that came from a gene.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

isONclust

:: MORE INFORMATION

Citation

Kristoffer Sahlin, Paul Medvedev (2019)
“De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm“,
RECOMB 2019

RepeatModeler 2.0.1 – de-novo Repeat Family Identification and Modeling package

RepeatModeler 2.0.1

:: DESCRIPTION

RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.

::DEVELOPER

RepeatModeler team – Institute for Systems Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RepeatModeler

:: MORE INFORMATION

Citation

PLoS One, 13 (3), e0193588 2018 Mar 14 eCollection 2018
Superior Ab Initio Identification, Annotation and Characterisation of TEs and Segmental Duplications From Genome Assemblies
Lu Zeng , R Daniel Kortschak , Joy M Raison , Terry Bertozzi , David L Adelson

Quartz 0.2 – de novo Quality Score Compression tool

Quartz 0.2

:: DESCRIPTION

Quartz (QUAlity score Reduction at Terabyte scale) is an efficient de novo quality score compression tool based on traversing the k-mer landscape of NGS read datasets.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Quartz

:: MORE INFORMATION

Citation:

Nat Biotechnol, 33 (3), 240-3 Mar 2015
Quality Score Compression Improves Genotyping Accuracy
Y William Yu, Deniz Yorukoglu , Jian Peng, Bonnie Berger

A5-miseq 20160825 – de novo Assembly & Analysis of Illumina Sequence data

A5-miseq 20160825

:: DESCRIPTION

de novo assembly & analysis of Illumina sequence data, including the A5 pipeline, A5-miseq, tools to evaluate assembly quality, and scripts to facilitate data submission to NCBI and the RAST annotation system

::DEVELOPER

The Darling Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 A5-miseq

:: MORE INFORMATION

Citation

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data.
Coil D, Jospin G, Darling AE.
Bioinformatics. 2014 Oct 22. pii: btu661.

PEAssember 1.2 – A de novo Genome Assembler

PEAssember 1.2

:: DESCRIPTION

PEAssember is a parallel de novo genome assembler for small – mid sized genomes.

::DEVELOPER

Pramila Nuwantha Ariyaratne, Sung Wing Kin, Ken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • C++ Compiler

:: DOWNLOAD

 PEAssember

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 15;27(2):167-74. doi: 10.1093/bioinformatics/btq626. Epub 2010 Dec 12.
PE-Assembler: de novo assembler using short paired-end reads.
Ariyaratne PN, Sung WK.

SEME 1.0 – A de novo Motif Finder for ChIP-seq data

SEME 1.0

:: DESCRIPTION

SEME ( Sampling with Expectation maximization for Motif Elicitation) is a de novo motif discovery algorithm  which uses pure probabilistic mixture model to model the motif’s binding features and uses expectation maximization (EM) algorithms to simultaneously learn the sequence motif, position, and sequence rank preferences without asking for any prior knowledge from the user.

::DEVELOPER

Sung Wing Kin, Ken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 SEME 

:: MORE INFORMATION

Citation

J Comput Biol. 2013 Mar;20(3):237-48. doi: 10.1089/cmb.2012.0233.
Simultaneously learning DNA motif along with its position and sequence rank preferences through expectation maximization algorithm.
Zhang Z, Chang CW, Hugo W, Cheung E, Sung WK.

Dimont – de-novo Motif Discovery tool

Dimont

:: DESCRIPTION

Dimont is a universal tool for de-novo motif discovery. Dimont has successfully been applied to ChIP-seq, ChIP-exo and protein-binding microarray (PBM) data.

::DEVELOPER

Jstacs Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 Dimont

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Nov;41(21):e197. doi: 10.1093/nar/gkt831. Epub 2013 Sep 20.
A general approach for discriminative de novo motif discovery from high-throughput data.
Grau J1, Posch S, Grosse I, Keilwagen J.

GibbsModule – Multispecies de novo Identification of Cis-regulatory Motifs and Modules

GibbsModule

:: DESCRIPTION

GibbsModule is a software for de novo detection of cis-regulatory motifs and modules in eukaryote genomes. GibbsModule models the coexpressed genes within one species as sharing a core cis-regulatory motif and each homologous gene group as sharing a homologous cis-regulatory module (CRM), characterized by a similar composition of motifs.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 GibbsModule

:: MORE INFORMATION

Citation

Genome Res. 2008 Aug;18(8):1325-35. Epub 2008 May 15.
Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells.
Xie D, Cai J, Chia NY, Ng HH, Zhong S.