:: 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
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
PhyloTrack is a JavaScript–based software tool that integrates the D3.js library for data visualization with the JBrowse tool for genome browser representation.
::DEVELOPER
:: SCREENSHOTS
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis.
Benavente ED, Coll F, Furnham N, McNerney R, Glynn JR, Campino S, Pain A, Mohareb FR, Clark TG.
BMC Bioinformatics. 2015 May 13;16:155. doi: 10.1186/s12859-015-0603-3.
:: DESCRIPTION
UPS-indel can be used to compare indels to see whether they are biologically equivalent or not. It can also be used to find out redundant indels.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hasan MS, Wu X, Watson LT, Zhang L.
UPS-indel: a Universal Positioning System for Indels.
Sci Rep. 2017 Oct 26;7(1):14106. doi: 10.1038/s41598-017-14400-1. PMID: 29074871; PMCID: PMC5658412.
:: DESCRIPTION
DiNuP compares the nucleosome profiles generated by high-throughput sequencing between different conditions. DiNuP provides a statistical p-value for each identified RDNP based on the difference of read distributions. DiNuP also empirically estimates the FDR as a cutoff when two samples have different sequencing depths and differentiate reliable RDNPs from the background noise. Evaluation of DiNuP showed it to be both sensitive and specific for the detection of changes in nucleosome location, occupancy and fuzziness. RDNPs that were identified using publicly available datasets revealed that nucleosome positioning dynamics are closely related to the epigenetic regulation of transcription.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Fu K, Tang Q, Feng J, Liu XS, Zhang Y.
DiNuP: a systematic approach to identify regions of differential nucleosome positioning.
Bioinformatics 2012; 28(15):1965-71.