title: Nsite, NsiteH and NsiteM computer tools for studying transcription regulatory elements.
abstract: Gene transcription is mostly conducted through interactions of various transcription factors and their binding sites on DNA (regulatory elements, REs). Today, we are still far from understanding the real regulatory content of promoter regions. Computer methods for identification of REs remain a widely used tool for studying and understanding transcriptional regulation mechanisms. The Nsite, NsiteH and NsiteM programs perform searches for statistically significant (non-random) motifs of known human, animal and plant one-box and composite REs in a single genomic sequence, in a pair of aligned homologous sequences and in a set of functionally related sequences, respectively.
  
  
  METHODS
  Pre-compiled executables built under commonly used operating systems are available for download by visiting http://www.molquest.kaust.edu.sa and http://www.softberry.com.
  
  
  BACKGROUND
  solovictor@gmail.com
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Computer, Electrical and Mathematical Sciences and Engineering Division, KAUST, Thuwal 23955-6900, KSA, Bioinformatics laboratory, Institute of Botany, ANAS, Baku AZ1073, Azerbaijan and.
authors.forename: Ilham A
authors.initials: IA
authors.lastname: Shahmuradov
authors.affiliation: Computer, Electrical and Mathematical Sciences and Engineering Division, KAUST, Thuwal 23955-6900, KSA, Bioinformatics Division, Softberry Inc., Mount Kisco, NY 10549, USA.
authors.forename: Victor V
authors.initials: VV
authors.lastname: Solovyev
mesh_terms: D000818:Animals; D001665:Binding Sites; D023281:Genomics; D006801:Humans; D059372:Nucleotide Motifs; D010944:Plants / Q000235:genetics; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors