:: DESCRIPTION
OpenGrowth is a research program which grows new ligands in proteins by connecting small organic fragments.
::DEVELOPER
The Shakhnovich Biophysics Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands.
Chéron N, Jasty N, Shakhnovich EI.
J Med Chem. 2015 Sep 23
:: DESCRIPTION
DNN-HMM (deep neural network and a hidden Markov model) is a novel hybrid architecture combining a pre-trained,for the de novo identification of replication domains using replication timing profiles.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
De novo Identification of replication-timing domains in the human genome by deep learning.
Liu F, Ren C, Li H, Zhou P, Bo X, Shu W.
Bioinformatics. 2015 Nov 5. pii: btv643.
:: DESCRIPTION
Telescoper is a local assembly algorithm designed for short-reads from NGS platforms such as Illumina. The reads must come from two libraries: one short insert, and one long insert.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bresler, M., Sheehan, S., Chan, A.H., and Song, Y.S.
Telescoper: De novo Assembly of Highly Repetitive Regions.
Bioinformatics, 28 (2012) i311-i317.
:: DESCRIPTION
TGNet is a Cytoscape-based tool for visualization and quality assessment of de novo genome assemblies. Specifically it facilitates rapid detection of inconsistencies between a genome assembly and an independently derived transcriptome assembly.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Dec 15;27(24):3425-6. doi: 10.1093/bioinformatics/btr569. Epub 2011 Oct 12.
Visualization and quality assessment of de novo genome assemblies.
Riba-Grognuz O, Keller L, Falquet L, Xenarios I, Wurm Y.
:: DESCRIPTION
LTRsift is a graphical desktop tool for semi-automatic postprocessing of de novo predicted LTR retrotransposon annotations, such as the ones generated by LTRharvest and LTRdigest.
::DEVELOPER
RESEARCH GROUP FOR GENOME INFORMATICS ,Center for Bioinformatics, University of Hamburg
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
S. Steinbiss, S. Kastens and S. Kurtz:
LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons.
Mobile DNA, 3:18 (2012)
:: DESCRIPTION
W-ChIPMotifs is a web application tool for de novo motif discovery from ChIP-based high throughput data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data.
Jin VX, Apostolos J, Nagisetty NS, Farnham PJ.
Bioinformatics. 2009 Dec 1;25(23):3191-3.
:: DESCRIPTION
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Li H.
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.
Bioinformatics. 2016 Jul 15;32(14):2103-10. doi: 10.1093/bioinformatics/btw152. Epub 2016 Mar 19. PMID: 27153593; PMCID: PMC4937194.
:: DESCRIPTION
DNMFilter is a machine learning based tool designed to filter out false positive de novo mutations (DNMs) obtained by any computational or manual approaches from next generation sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Mar 27.
A gradient-boosting approach for filtering de novo mutations in parent-offspring trios.
Liu Y1, Li B, Tan R, Zhu X, Wang Y.
:: DESCRIPTION
Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms. It achieves this by using an array of hash lengths, a dynamic filtering of noise, a robust resolution of alternative splicing events, and the efficient merging of multiple assemblies. It was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Marcel H. Schulz, Daniel R. Zerbino, Martin Vingron and Ewan Birney
Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels
Bioinformatics (2012)doi: 10.1093/bioinformatics/bts094
:: DESCRIPTION
MonSTR is a tool for calling de novo mutations from HipSTR or GangSTR VCF files.)
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mitra I, Huang B, Mousavi N, Ma N, Lamkin M, Yanicky R, Shleizer-Burko S, Lohmueller KE, Gymrek M.
Patterns of de novo tandem repeat mutations and their role in autism.
Nature. 2021 Jan;589(7841):246-250. doi: 10.1038/s41586-020-03078-7. Epub 2021 Jan 13. PMID: 33442040; PMCID: PMC7810352.