DNAzip statistics

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Tool usage distribution map

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Associated diseases

Associated diseases

DNAzip specifications

Information


Unique identifier OMICS_00954
Name DNAzip
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Reference genome, reference SNP map, and genome to be compressed
Input format FASTA
Output data compressed genome
Output format TXT
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Requirements
GNU C++
Maintained Yes

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Publications for DNAzip

DNAzip in publications

 (3)
PMCID: 4493149
PMID: 26146838
DOI: 10.1371/journal.pone.0132460

[…] data can be 400× smaller than the original. non-referential approaches achieve ratios of up to 8:1 []., several tools implement referential compression, and some of them are noteworthy, namely: dnazip [], rlz [], gdc [] and fresco []. dnazip is one of the pioneers in this approach, and the other mentioned solutions optimized and advanced the topic at their launching time. the main […]

PMCID: 2964686
PMID: 20946637
DOI: 10.1186/1471-2105-11-514

[…] [] consider the task of directly compressing large sequence strings. while others consider alternative compression tasks such as coil [] which compresses a large database of unrelated sequences or dnazip [] which compresses variations to a reference genome. our goal is different as we want to compress a large number of very short sequences while using a large reference sequence. whether […]

PMCID: 2706893
PMID: 19534804
DOI: 10.1186/1471-2164-10-270

[…] systematically ranked in the top 5 of genes de throughout parasite development (see additional file ). however, the same er-stress induced complex, involving atf4, which binds to ddit3 through a dnazip binding domain, has been shown to regulate the heme oxygenase 1 (hmox-1) gene expression as a defense mechanism against oxidative stress []. interestingly, atf4 is also up-regulated […]


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DNAzip institution(s)
Department of Mathematics and Informatics, University of Palermo, Palermo, Italy; Computational Genomics Group, IBM T J Watson Research Center, Yorktown, NY, USA

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