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DNA
2005
Springer
144views Bioinformatics» more  DNA 2005»
13 years 10 months ago
Designing Nucleotide Sequences for Computation: A Survey of Constraints
We survey the biochemical constraints useful for the design of DNA code words for DNA computation. We define the DNA/RNA Code Constraint problem and cover biochemistry topics rel...
Jennifer A. Sager, Darko Stefanovic
CANDC
2008
ACM
13 years 4 months ago
'Genome order index' should not be used for defining compositional constraints in nucleotide sequences
Background: The Z-curve is a three dimensional representation of DNA sequences proposed over a decade ago and has been extensively applied to sequence segmentation, horizontal gen...
Eran Elhaik, Dan Graur, Kresimir Josic
NAR
2007
106views more  NAR 2007»
13 years 4 months ago
INFO-RNA - a server for fast inverse RNA folding satisfying sequence constraints
INFO-RNA is a new web server for designing RNA sequences that fold into a user given secondary structure. Furthermore, constraints on the sequence can be specified, e.g. one can r...
Anke Busch, Rolf Backofen
BMCBI
2010
148views more  BMCBI 2010»
13 years 4 months ago
Calling SNPs without a reference sequence
Background: The most common application for the next-generation sequencing technologies is resequencing, where short reads from the genome of an individual are aligned to a refere...
Aakrosh Ratan, Yu Zhang, Vanessa M. Hayes, Stephan...
BMCBI
2008
104views more  BMCBI 2008»
13 years 4 months ago
ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS)
Background: Genome survey sequences (GSS) offer a preliminary global view of a genome since, unlike ESTs, they cover coding as well as non-coding DNA and include repetitive region...
Thomas D. Otto, Leonardo H. F. Gomes, Marcelo Alve...