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SymCurv specifications

Information


Unique identifier OMICS_16872
Name SymCurv
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A DNA sequence.
Input format FASTA
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 20
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Christoforos Nikolaou <>

SymCurv citations

 (3)
library_books

Inter locus as well as intra locus heterogeneity in LINE 1 promoter methylation in common human cancers suggests selective demethylation pressure at specific CpGs

2015
PMCID: 4367886
PMID: 25798207
DOI: 10.1186/s13148-015-0051-y

[…] for a consensus line sequence derived from the 11 individual sequences analyzed in this study. nucleosome positioning predictions were done using three methods: 1) a freely available web server (symcurv at http://genome.crg.es/cgi-bin/symcurv/symcurv_borinot.pl/accessed on 31/08/2013) which works on the basis of dna curvature, 2) experimental nucleosome probability data available […]

library_books

Topoisomerase II regulates yeast genes with singular chromatin architectures

2013
PMCID: 3814376
PMID: 23935120
DOI: 10.1093/nar/gkt707

[…] tss. relative occupancies for ‘appearing’, ‘evicted’ and ‘fragile’ nucleosomes were presented as mean percentage of overlap of the genomic region., theoretical nucleosome affinity was performed with symcurv (), an ab initio algorithm based on the concept of the symmetry of dna curvature. briefly, symcurv values were calculated at nucleotide resolution for a given dna sequence as a score […]

library_books

Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae

2010
PMCID: 2994855
PMID: 21073701
DOI: 10.1186/1756-8935-3-20

[…] work [], we introduced a structural property that quantifies the strength of the pattern described above. we implemented this concept ('symmetry of dna curvature') in a suitably adjusted method (symcurv), which permits us to attribute a symmetry of curvature score to each nucleotide on a given dna sequence (see methods for details). we calculated symcurv for the complete genome sequence […]


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