:: DESCRIPTION
NSeq is a multithreaded Java application for finding positioned nucleosomes from sequencing data
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
A. Nellore, K. Bobkov, E. Howe, A. Pankov, A. Diaz, J.S. Song.
NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data,
Frontiers in Genetics, 3:320 (2013)
:: DESCRIPTION
NUCwave is a bioinformatic tool that generates nucleosome occupation maps.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Brief Bioinform. 2014 Oct 8. pii: bbu037
Comparative analysis of methods for genome-wide nucleosome cartography.
Quintales L, Vázquez E, Antequera F.
:: DESCRIPTION
nuMap implements the YR and W/S schemes to predict nucleosome positioning at high resolution.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
nuMap: a web platform for accurate prediction of nucleosome positioning.
Alharbi BA, Alshammari TH, Felton NL, Zhurkin VB, Cui F.
Genomics Proteomics Bioinformatics. 2014 Oct;12(5):249-53. doi: 10.1016/j.gpb.
:: DESCRIPTION
FineStr (pronounced as (fi-nes’tru), from Latin fenestra—window, and from fine structure]) server allows users to upload genomic sequences in FASTA format and to perform a single-base-resolution nucleosome mapping on them.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Bioinformatics. 2010 Mar 15;26(6):845-6. doi: 10.1093/bioinformatics/btq030. Epub 2010 Jan 26.
FineStr: a web server for single-base-resolution nucleosome positioning.
Gabdank I1, Barash D, Trifonov EN.
:: DESCRIPTION
FFN is a pattern discovery and scoring algorithm to identify feature patterns that are differentially enriched in nucleosome-forming sequences and nucleosome-depletion sequences
::DEVELOPER
Hu Lab – Data Integration and Knowledge Discovery @ UCF
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Genomics. 2014 Jul 23. pii: S0888-7543(14)00117-7. doi: 10.1016/j.ygeno.2014.07.002. [Epub ahead of print]
Computational discovery of feature patterns in nucleosomal DNA sequences.
Zheng Y, Li X, Hu H
:: DESCRIPTION
NPS (Nucleosome Positioning from Sequencing) is a signal processing-based algorithm for identifying positioned nucleosomes fromsequencing experiments at the nucleosome level.The software is a python software package that can identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level. NPS obtains continuous wave-form that represents the enrichment of histone modifications (or nucleosomes) by extending each tag (25nt, Solexa) to 150nt in the 3’ direction and taking the middle 75, and detects the positions of nucleosomes based on Laplacian of Gaussian (LOG) edge detection. The p value of each detection was estimated using Poisson approximation and the user can decide a cut-off for the final selection of nucleosome positions. In case of histone modification, the sequence tags are regrouped by different types of histone modification after nucleosome positioning and then the p-value of a particular histone modification at a positioned nucleosome was calculated based on the tag count of that histone modification in the nucleosome region using Poisson distribution, similar to the method mentioned above. The user also can select a cut-off of p value in histone modification assignment.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Zhang Y, Shin H, Song JS, Lei Y, Liu XS.
Identifying Positioned Nucleosomes with Epigenetic Marks in Human from ChIP-Seq.
BMC Genomics 2008, 9:537.
:: DESCRIPTION
Nucleosome is web-based nucleosome map visual browser backed up by BWT-based pattern searches. It can be used for other kinds of high-throughput genomic data as well.
::DEVELOPER
The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Santamaría, R., Therón, R., Durán, L., García, A., González, S., Sánchez, M., & Antequera, F. (2019).
Genome-wide search of nucleosome patterns using visual analytics.
Bioinformatics, 35(13), 2185-2192
:: DESCRIPTION
iNuc-force allows for discriminating nucleosome-enriched regions from nucleosome-depleted regions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
DNA physical properties outperform sequence compositional information in classifying nucleosome-enriched and -depleted regions.
Liu G, Liu GJ, Tan JX, Lin H.
Genomics. 2019 Sep;111(5):1167-1175. doi: 10.1016/j.ygeno.2018.07.013.
:: DESCRIPTION
iNuc-PhysChem is a sequence-based predictor for identifying nucleosomes via physicochemical properties
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
PLoS One. 2012;7(10):e47843. doi: 10.1371/journal.pone.0047843. Epub 2012 Oct 29.
iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties.
Chen W1, Lin H, Feng PM, Ding C, Zuo YC, Chou KC.
:: DESCRIPTION
The web-server iNuc-PseKNC was developed to predict nucleosome occupancy of H. sapiens, C. elegan and D. melanogaster
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition.
Guo SH, Deng EZ, Xu LQ, Ding H, Lin H, Chen W, Chou KC.
Bioinformatics. 2014 Jun 1;30(11):1522-9. doi: 10.1093/bioinformatics/btu083.