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D2Z specifications

Information


Unique identifier OMICS_14303
Name D2Z
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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  • person_outline Saurabh Sinha <>

Publication for D2Z

D2Z in publications

 (4)
PMCID: 4989896
PMID: 27535823
DOI: 10.1186/s12920-016-0193-6

[…] ge{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}${d_{2}^{z}}$\end{document}d2z is defined as: \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsf […]

PMCID: 3289921
PMID: 22247280
DOI: 10.1093/bioinformatics/bts028

[…] as an estimation of the length of the repeat-free sequence. repeat-masked sequences are treated equally for all methods. note that this is slightly different to the original method proposed for d2z, which introduced artificial words by concatenating sequences., genome-wide datasets consist of many thousand regulatory sequences. the computation of pairwise similarities needs to be efficient […]

PMCID: 2631479
PMID: 19128496
DOI: 10.1186/1471-2164-10-9

[…] pairs there are additional but unidentified relevant sequence motifs. in order to get around these twin difficulties, we compared how similar the full set of promoter pairs were to one another using d2z scores. the d2z score is an alignment-free sequence comparison metric which compares k-mer word distributions between two sequences []. the alternative promoter pairs of genes with exactly two […]

PMCID: 2395258
PMID: 18226245
DOI: 10.1186/gb-2008-9-1-r22

[…] called 'simulated annealing' (see materials and methods). we also experimented with a different search strategy, namely, 'gibbs sampling' in conjunction with the same scoring scheme., in the d2z-set method, we make use of our previous work [] on measuring the similarity between any two regulatory sequences based on their word frequency distributions. in a set of functionally related crms […]


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D2Z institution(s)
Department of Computer Science, University of Illinois, Urbana-Champaign, IL, USA; Department of Entomology, University of Illinois, Urbana-Champaign, IL, USA; Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL, USA
D2Z funding source(s)
This work was funded in part by Illinois Sociogenomics Initiative.

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