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» Structural Alignment of Pseudoknotted RNA
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BMCBI
2005
125views more  BMCBI 2005»
13 years 7 months ago
Multiple sequence alignments of partially coding nucleic acid sequences
Background: High quality sequence alignments of RNA and DNA sequences are an important prerequisite for the comparative analysis of genomic sequence data. Nucleic acid sequences, ...
Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried,...
BMCBI
2004
96views more  BMCBI 2004»
13 years 7 months ago
Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides
Background: Computer programs for the generation of multiple sequence alignments such as "Clustal W" allow detection of regions that are most conserved among many sequen...
Olga V. Matveeva, Brian T. Foley, Vladimir A. Nemt...
WABI
2007
Springer
121views Bioinformatics» more  WABI 2007»
14 years 1 months ago
Seeded Tree Alignment and Planar Tanglegram Layout
The optimal transformation of one tree into another by means of elementary edit operations is an important algorithmic problem that has several interesting applications to computat...
Antoni Lozano, Ron Y. Pinter, Oleg Rokhlenko, Gabr...
BMCBI
2007
226views more  BMCBI 2007»
13 years 7 months ago
MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans
Background: MicroRNAs (miRNAs) are recognized as one of the most important families of noncoding RNAs that serve as important sequence-specific post-transcriptional regulators of ...
Ting-Hua Huang, Bin Fan, Max F. Rothschild, Zhi-Li...
GCB
2006
Springer
119views Biometrics» more  GCB 2006»
13 years 11 months ago
Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs
: The analysis of small circular sequences requires specialized tools. While the differences between linear and circular sequences can be neglected in the case of long molecules su...
Axel Mosig, Ivo L. Hofacker, Peter F. Stadler