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RECOMB
2004
Springer
14 years 10 months ago
Designing multiple simultaneous seeds for DNA similarity search
The challenge of similarity search in massive DNA sequence databases has inspired major changes in BLAST-style alignment tools, which accelerate search by inspecting only pairs of...
Yanni Sun, Jeremy Buhler
ISMB
1996
13 years 11 months ago
Improving the Quality of Automatic DNA Sequence Assembly Using Fluorescent Trace-Data Classifications
Virtually all large-scale sequencing projects use automatic sequence-assembly programs to aid in the determination of DNA sequences. The computer-generated assemblies require subs...
Carolyn F. Allex, Schuyler F. Baldwin, Jude W. Sha...
COMPLEX
2009
Springer
13 years 11 months ago
Moving Breather Collisions in the Peyrard-Bishop DNA Model
We consider collisions of moving breathers (MBs) in the Peyrard-Bishop DNA model. Two identical stationary breathers, separated by a fixed number of pair-bases, are perturbed and b...
A. Alvarez, F. R. Romero, J. Cuevas, J. F. R. Arch...
RECOMB
2003
Springer
14 years 10 months ago
Designing seeds for similarity search in genomic DNA
Large-scale comparison of genomic DNA is of fundamental importance in annotating functional elements of genomes. To perform large comparisons efficiently, BLAST (Methods: Companio...
Jeremy Buhler, Uri Keich, Yanni Sun
IPPS
2003
IEEE
14 years 3 months ago
A Fast Algorithm for the Exhaustive Analysis of 12-Nucleotide-Long DNA Sequences. Applications to Human Genomics
We have developed a new algorithm that allows the exhaustive determination of words of up to 12 nucleotides in DNA sequences. It is fast enough as to be used at a genomic scale ru...
Vicente Arnau, Ignacio Marín