• iNuc-PseKNC

  • Referenced in 31 articles [sw16607]
  • sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition ... Motivation: Nucleosome positioning participates in many cellular activities and plays significant roles in regulating cellular ... methods for rapidly and effectively identifying nucleosome positioning. Although some computational methods were proposed, most ... play important roles in determining the nucleosome positioning on a DNA sequence. Results: Here...
  • iNuc-PhysChem

  • Referenced in 24 articles [sw22453]
  • identifying nucleosomes via physicochemical properties. Nucleosome positioning has important roles in key cellular processes. Although ... this area, the rules defining nucleosome positioning is still elusive and debated. In this study ... twelve DNA physicochemical features between the nucleosomal and linker sequences in the Saccharomyces ... cerevisiae genome. We found that nucleosomal sequences have some position-specific physicochemical features, which...
  • iNuc-STNC

  • Referenced in 5 articles [sw25364]
  • sequence-based predictor for identification of nucleosome positioning in genomes by extending the concept ... order to identify accurately and reliably nucleosome positioning in genomes. In this proposed model...
  • NucPosPred

  • Referenced in 2 articles [sw24770]
  • NucPosPred: predicting species-specific genomic nucleosome positioning via four different modes of general PseKNC ... genomes should be investigated. High-resolution nucleosome-positioning maps are now available for organisms including ... Caenorhabditis elegans}, enabling the identification of nucleosome positioning by application of computational tools. Here ... designed for large-scale identification of nucleosome positioning in {it C. elegans...
  • iNuc-ext-PseTNC

  • Referenced in 1 article [sw27672]
  • efficient ensemble model for identification of nucleosome positioning by extending the concept of Chou ... transcriptional regulation formation. Identification of nucleosome positioning via wet lab is difficult; so, the attention ... PseTNC” is developed to identify the nucleosome positioning in genomes accurately. In this predictor...
  • nucleR

  • Referenced in 1 article [sw22389]
  • package nucleR: Nucleosome positioning package for R. Nucleosome positioning for Tiling Arrays and NGS experiments...
  • ThIEF

  • Referenced in 1 article [sw33129]
  • comparing multiple genome-wide maps representing nucleosome positions or specific histone marks. These maps ... list of genomics locations for nucleosomes or histone marks. The output is an alignment ... applications on the analysis of temporal nucleosome maps for the human malaria parasite ... that can accurately predict the position of stable nucleosomes (i.e., nucleosomes present in all time...
  • PING

  • Referenced in 0 articles [sw32043]
  • PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data. MNase ... identify enriched regions, software tools for nucleosome positioning are still limited. We introduce a flexible ... source R package, PING 2.0, for nucleosome positioning using MNase-Seq data or MNase ... uses a model-based approach, which enables nucleosome predictions even in the presence...
  • nucleoSim

  • Referenced in 1 article [sw22391]
  • synthetic map with reads covering the nucleosome regions as well as a synthetic map with ... between three different distributions for the read positioning: Normal, Student and Uniform...
  • R

  • Referenced in 9832 articles [sw00771]
  • R is a language and environment for statistical...
  • GLPK

  • Referenced in 181 articles [sw04560]
  • The GLPK (GNU Linear Programming Kit) package is...
  • LIBSVM

  • Referenced in 1185 articles [sw04879]
  • LIBSVM is a library for Support Vector Machines...
  • Stata

  • Referenced in 837 articles [sw06029]
  • Stata is a complete, integrated statistical package that...
  • BioProspector

  • Referenced in 29 articles [sw09375]
  • BioProspector: discovering conserved DNA motifs in upstream regulatory...
  • ClustalW

  • Referenced in 138 articles [sw12016]
  • CLUSTAL W: improving the sensitivity of progressive multiple...
  • MUSCLE

  • Referenced in 74 articles [sw13193]
  • Muscle: multiple sequence alignment with high accuracy and...
  • KEGG

  • Referenced in 275 articles [sw13866]
  • KEGG: Kyoto Encyclopedia of Genes and Genomes. KEGG...
  • pSuc-Lys

  • Referenced in 31 articles [sw16643]
  • pSuc-Lys: predict lysine succinylation sites in proteins...
  • JASPAR

  • Referenced in 42 articles [sw18502]
  • JASPAR: an open‐access database for eukaryotic transcription...